FAS Research Computing | Knowledgebase

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/2metdb:

      bio/2metdb
      ****************************************************

       This module sets up the environment for:

       2metdb version 1.2
       genome scanning for secondary metabolite pathways

       Use the command:

       module display bio/2metdb

       to see exactly what this module does.
run by : 2metdb path_to_multifasta_peptide_file > ~/filename.html

      ****************************************************

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updated: 4/02/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/454_util:

      bio/454_util
      ****************************************************

       This module sets up the environment for:

       454 utilities
       454 utilities

       Use the command:

       module display bio/454_util

       to see exactly what this module does.

      ****************************************************

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updated: 5/27/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ABCreg:

      bio/ABCreg
      ****************************************************

       This module sets up the environment for:

       ABCreg
       Implements the linear regression approach to Approximate Bayesian Computation, or ABC

       Use the command:

       module display bio/ABCreg

       to see exactly what this module does.

      ****************************************************

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updated: 7/13/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/AmberTools12:

      bio/AmberTools12
      ****************************************************

       This module sets up the environment for:

       AmberTools version 12
       AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations (using NAB or mdgx), with either explicit water or generalized Born solvent models. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/AmberTools12

       to see exactly what this module does.

      ****************************************************

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updated: 4/24/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BEDTools-2.11.2:

      bio/BEDTools-2.11.2
      ****************************************************

       This module sets up the environment for:

       BEDTools version 2.11.2
       utilities for manipulating alignments in the BED, sam, and bam format

       Use the command:

       module display bio/BEDTools-2.11.2

       to see exactly what this module does.

      ****************************************************

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updated: 2/27/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BEDTools-2.17.0:

      bio/BEDTools-2.17.0
      ****************************************************

       This module sets up the environment for:

       BEDTools version 2.17.0
       utilities for manipulating alignments in the BED, sam, and bam format

       Use the command:

       module display bio/BEDTools-2.17.0

       to see exactly what this module does.

      ****************************************************

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updated: 2/20/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesCall-0.3:

      bio/BayesCall-0.3
      ****************************************************

       This module sets up the environment for:

       BayesCall version 0.3
       A model-based basecalling algorithm for high-throughput short-read sequencing

       Use the command:

       module display bio/BayesCall-0.3

       to see exactly what this module does.

      ****************************************************

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updated: 11/19/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies-1.1:

      bio/BayesPhylogenies-1.1
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies v.1.1
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display bio/BayesPhylogenies-1.1

       to see exactly what this module does.

      ****************************************************

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updated: 8/10/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies-1.1_openmp:

      bio/BayesPhylogenies-1.1_openmp
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 1.1, OpenMP-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display bio/BayesPhylogenies-1.1_openmp

       to see exactly what this module does.

      ****************************************************

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updated: 9/09/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies-1.1_openmpi-1.3.2_intel-11.0.083:

      bio/BayesPhylogenies-1.1_openmpi-1.3.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 1.1, MPI-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display bio/BayesPhylogenies-1.1_openmpi-1.3.2_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

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updated: 9/09/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies-2.0.2_openmpi-1.4.2_intel-11.1.072:

      bio/BayesPhylogenies-2.0.2_openmpi-1.4.2_intel-11.1.072
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 2.0.2, MPI-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/BayesPhylogenies-2.0.2_openmpi-1.4.2_intel-11.1.072

       to see exactly what this module does.

      ****************************************************

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updated: 7/10/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies-2.0.2_openmpi-1.6.2_intel-13.0.079:

      bio/BayesPhylogenies-2.0.2_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 2.0.2, MPI-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/BayesPhylogenies-2.0.2_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

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updated: 4/24/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies_MPI_V2.0Beta_01_06_2012:

      bio/BayesPhylogenies_MPI_V2.0Beta_01_06_2012
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 2.0, MPI-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display bio/BayesPhylogenies_MPI_V2.0Beta_01_06_2012

       to see exactly what this module does.

      ****************************************************

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updated: 1/06/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesPhylogenies_MPI_V2.0Beta_12_13_2010:

      bio/BayesPhylogenies_MPI_V2.0Beta_12_13_2010
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies version 2.0, MPI-enabled
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display bio/BayesPhylogenies_MPI_V2.0Beta_12_13_2010

       to see exactly what this module does.

      ****************************************************

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updated: 12/13/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BayesTraitsV2:

      bio/BayesTraitsV2
      ****************************************************

       This module sets up the environment for:

       BayesTraits version 2
       a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/BayesTraitsV2

       to see exactly what this module does.

      ****************************************************

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updated: 12/18/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BclConverter-1.7.1:

      bio/BclConverter-1.7.1
      ****************************************************

       This module sets up the environment for:

       CASAVA-1.7.0
       Consensus Assessment of Sequence And VAriation, formerly GA-Pipeline, version 1.7.0

       Use the command:

       module display bio/BclConverter-1.7.1

       to see exactly what this module does.

      ****************************************************

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updated: 12/04/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BioPerl-1.6.1:

      bio/BioPerl-1.6.1
      ****************************************************

       This module sets up the environment for:

       BioPerl 1.6.1
       a collection of Perl modules for bioinformatics

       Use the command:

       module display bio/BioPerl-1.6.1

       to see exactly what this module does.

      ****************************************************

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updated: 7/21/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/BioPerl-1.6.901:

      bio/BioPerl-1.6.901
      ****************************************************

       This module sets up the environment for:

       BioPerl 1.6.901
       a collection of Perl modules for bioinformatics

       Use the command:

       module display bio/BioPerl-1.6.901

       to see exactly what this module does.

      ****************************************************

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updated: 7/31/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/CAP3:

      bio/CAP3
      ****************************************************

       This module sets up the environment for:

       SAM Tools version 0.1.18
       utilities for manipulating alignments in the Sequence Alignment/Map format

       Use the command:

       module display bio/CAP3

       to see exactly what this module does.

      ****************************************************

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updated: 3/26/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/CASAVA-1.7.0:

      bio/CASAVA-1.7.0
      ****************************************************

       This module sets up the environment for:

       CASAVA-1.7.0
       Consensus Assessment of Sequence And VAriation, formerly GA-Pipeline, version 1.7.0

       Use the command:

       module display bio/CASAVA-1.7.0

       to see exactly what this module does.

      ****************************************************

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updated: 11/19/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/CASAVA-1.8.1:

      bio/CASAVA-1.8.1
      ****************************************************

       This module sets up the environment for:

       CASAVA-1.8.1
       Consensus Assessment of Sequence And VAriation, formerly GA-Pipeline, version 1.8.1

       Use the command:

       module display bio/CASAVA-1.8.1

       to see exactly what this module does.

      ****************************************************

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updated: 8/03/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/CASAVA-1.8.2:

      bio/CASAVA-1.8.2
      ****************************************************

       This module sets up the environment for:

       CASAVA-1.8.2
       Consensus Assessment of Sequence And VAriation, formerly GA-Pipeline, version 1.8.2

       Use the command:

       module display bio/CASAVA-1.8.2

       to see exactly what this module does.

      ****************************************************

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updated: 3/05/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/COAL-11:

      bio/COAL-11
      ****************************************************

       This module sets up the environment for:

       COAL Uploaded 11 Jan 2009
       Program for computing gene tree probabilities and simulating gene trees in species trees under the coalescent model. http://www.coaltree.net/coalhome.html

       Use the command:

       module display bio/COAL-11

       to see exactly what this module does.

      ****************************************************

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updated: 10/06/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ClonalFrame-1.2:

      bio/ClonalFrame-1.2
      ****************************************************

       This module sets up the environment for:

       ClonalFrame, version 1.2
       Package for the inference of bacterial microevolution using multilocus sequence data

       Use the command:

       module display bio/ClonalFrame-1.2

       to see exactly what this module does.

      ****************************************************

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updated: 3/06/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/Corona_Lite_4.2.2:

      bio/Corona_Lite_4.2.2
      ****************************************************

       This module sets up the environment for:

       Corona Lite Version 4.2.2
       The SOLiD. System Analysis Pipeline Tool is an off-instrument SOLiD data analysis software package

       Use the command:

       module display bio/Corona_Lite_4.2.2

       to see exactly what this module does.

      ****************************************************

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updated: 12/09/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/DaliLite_3.3:

      DaliLite_3.3 module
      ****************************************************

       This module sets up the following environment
       variables for DaliLite_3.3:
       PATH
      ****************************************************

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updated: 7/30/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/FungalITSPipeline:

      bio/FungalITSPipeline
      ****************************************************

       This module sets up the environment for:

       FungalITSPipeline
       A software pipeline for processing and identification of fungal ITS sequences

       Use the command:

       module display bio/FungalITSPipeline

       to see exactly what this module does.

      ****************************************************

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updated: 7/29/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK:

      bio/GenomeAnalysisTK
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 1.1-37
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-1.1-37/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 10/05/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK-2.0-39:

      bio/GenomeAnalysisTK-2.0-39
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 1.1-37
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK-2.0-39

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-2.0-39-gd091f72/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 8/15/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK-2.1-11:

      bio/GenomeAnalysisTK-2.1-11
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 2.1-11
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK-2.1-11

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-2.1-11/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 10/04/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK-2.3-4:

      bio/GenomeAnalysisTK-2.3-4
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 2.3-4
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK-2.3-4

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 12/27/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK-2.3-9:

      bio/GenomeAnalysisTK-2.3-9
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 2.3-9
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK-2.3-9

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 2/20/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeAnalysisTK-2.4.3:

      bio/GenomeAnalysisTK-2.4.3
      ****************************************************

       This module sets up the environment for:

       The Genome Analysis Toolkit (GATK),version 2.4.3
       The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

       Use the command:

       module display bio/GenomeAnalysisTK-2.4.3

       to see exactly what this module does.
run by :java -jar /n/sw/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar --help
JVM argument -Xmx2g is recommended
      ****************************************************

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updated: 2/28/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/GenomeMapper-0.4.15:

      bio/GenomeMapper-0.4.15
      ****************************************************

       This module sets up the environment for:

       GenomeMapper 0.4.15
       GenomeMapper is a short read mapping tool designed for accurate read alignments

       Use the command:

       module display bio/GenomeMapper-0.4.15

       to see exactly what this module does.

      ****************************************************

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updated: 3/30/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/HyperLasso:

      bio/HyperLasso
      ****************************************************

       This module sets up the environment for:

       HyperLasso
       HyperLasso - simultaneous analysis of many SNPs and covariates

       Use the command:

       module display bio/HyperLasso

       to see exactly what this module does.



      ****************************************************

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updated: 3/31/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MACS-1.3.5:

      MACS-1.3.5 module
      ****************************************************

       This module sets up the following environment
       variables for MACS version 1.3.5:
       PATH
       MANPATH

      ****************************************************

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updated: 7/31/2011

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MACS-1.3.5_nopython:

      MACS-1.3.5 module
      ****************************************************

       This module sets up the following environment
       variables for MACS version 1.3.5:
       PATH
       MANPATH

      ****************************************************

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updated: 7/29/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MACS-1.4.2-1:

      bio/MACS-1.4.2-1
      ****************************************************

       This module sets up the environment for:

       Model-based Analysis of ChIP-Seq, version 1.4.2-1
       a novel algorithm for identifying transcript factor binding sites

       Use the command:

       module display bio/MACS-1.4.2-1

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

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updated: 3/08/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MACS-2.0.10.20130306:

      bio/MACS-2.0.10.20130306
      ****************************************************

       This module sets up the environment for:

       Model-based Analysis of ChIP-Seq, version 2.0.10.20130306
       a novel algorithm for identifying transcript factor binding sites

       Use the command:

       module display bio/MACS-2.0.10.20130306

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

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updated: 3/08/2013

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MCMCcoal-1.2:

      bio/MCMCcoal-1.2
      ****************************************************

       This module sets up the environment for:

       MCMCcoal Version 1.2 December 2007
       A Bayesian MCMC Coalescent Program. http://abacus.gene.ucl.ac.uk/software/MCMCcoal.html

       Use the command:

       module display bio/MCMCcoal-1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/06/2009

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MOSAIK-2.1.33:

      bio/MOSAIK-2.1.33
      ****************************************************

       This module sets up the environment for:

       MOSAIK-2.1.33
       MOSAIK is a reference-guided assembler comprising of four main modular programs

       Use the command:

       module display bio/MOSAIK-2.1.33

       to see exactly what this module does.

      ****************************************************

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updated: 1/23/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MUMmer3.23:

      bio/MUMmer3.23
      ****************************************************

       This module sets up the environment for:

       MUMmer version 3.23
       a system for rapidly aligning entire genomes, whether in complete or draft form. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/MUMmer3.23

       to see exactly what this module does.

      ****************************************************

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updated: 6/15/2012

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MaToGff:

      bio/MaToGff
      ****************************************************

       This module sets up the environment for:

       MaToGff
       SOLiD. System GFF Conversion Tool (matogff)

       Use the command:

       module display bio/MaToGff

       to see exactly what this module does.

      ****************************************************

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updated: 1/14/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MapSplice_1.14.1:

      bio/MapSplice_1.14.1
      ****************************************************

       This module sets up the environment for:

       MapSplice version 1.14.1
       Accurate mapping of RNA-seq reads for splice junction discovery

       Use the command:

       module display bio/MapSplice_1.14.1

       to see exactly what this module does.

      ****************************************************

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updated: 12/10/2010

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Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/MetaVelvet-1.1.01:

      bio/MetaVelvet-1.1.01
      ****************************************************

       This module sets up the environment for:

       MetaVelvet-1.1.01
       a de novo genomic assembler specially designed for short read sequencing technologiesi for metagenomics

       Use the command:

       module display bio/MetaVelvet-1.1.01

       to see exactly what this module does.

      ****************************************************

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updated: 11/06/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/NGSQCToolkit_v2.3:

      bio/NGSQCToolkit_v2.3
      ****************************************************

       This module sets up the environment for:

       NGS QC Toolkit version 2.3
       A toolkit for the quality control (QC) of next generation sequencing (NGS) data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/NGSQCToolkit_v2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/Ne3sML-1.1:

      bio/Ne3sML-1.1
      ****************************************************

       This module sets up the environment for:

       Ne3sML Version 1.2
       Ne3sML program implements the ML method of Yang (2002). The program uses numerical integration routines in Mathematica so you have to have Mathematica 3.0 or later to run the program. http://abacus.gene.ucl.ac.uk/software/MCMCcoal.html

       Use the command:

       module display bio/Ne3sML-1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/06/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/OLB-1.8.0:

      bio/OLB-1.8.0
      ****************************************************

       This module sets up the environment for:

       OLB-1.8.0
       GenomeAnalyzer Off-line Base Caller, a.k.a. Solexa pipeline, formerly GA-Pipeline, version 1.8.0

       Use the command:

       module display bio/OLB-1.8.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/18/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/OLB-1.9.0:

      bio/OLB-1.9.0
      ****************************************************

       This module sets up the environment for:

       OLB-1.9.0
       GenomeAnalyzer Off-line Base Caller, a.k.a. Solexa pipeline, formerly GA-Pipeline, version 1.9.0

       Use the command:

       module display bio/OLB-1.9.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/OLB-1.9.4:

      bio/OLB-1.9.4
      ****************************************************

       This module sets up the environment for:

       OLB-1.9.4
       GenomeAnalyzer Off-line Base Caller, a.k.a. Solexa pipeline, formerly GA-Pipeline, version 1.9.4

       Use the command:

       module display bio/OLB-1.9.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/OMA:

      bio/OMA
      ****************************************************

       This module sets up the environment for:

       OMA
       The OMA algorithm uses as input the sequences from complete genomes and yields orthologous relations and groups of orthologs. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/OMA

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/OligoArray2_1:

      bio/OligoArray2_1
      ****************************************************

       This module sets up the environment for:

       OligoArray2_1
       OligoArray is a program that computes gene specific oligonucleotides that are free of secondary structure for genome-scale oligonucleotide microarray construction. This module has been built by Mike Ethier.

       Use the command:

       module display bio/OligoArray2_1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/17/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/PBJelly_12.9.14:

      bio/PBJelly_12.9.14
      ****************************************************

       This module sets up the environment for:

       PBJelly version 12.9.14
       This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/PBJelly_12.9.14

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/19/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/PRGmatic_PE.v1.5:

      bio/PRGmatic_PE.v1.5
      ****************************************************

       This module sets up the environment for:

       PRGmatic_PE version 1.5
       Pipeline for handling paired-end Next-Gen sequence data.

       Use the command:

       module display bio/PRGmatic_PE.v1.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/31/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ParsInsert-1.04:

      bio/ParsInsert-1.04
      ****************************************************

       This module sets up the environment for:

       ParsInsert version 1.04
       ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/ParsInsert-1.04

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/PhyloCSF:

      bio/PhyloCSF
      ****************************************************

       This module sets up the environment for:

       PhyloCSF
       a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/PhyloCSF

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/QuEST_2.4:

      QuEST_2.4 module
      ****************************************************

       This module sets up the environment PATH
       variables for QuEST_2.4:
       QuEST is a statistical software for analysis of ChIP-Seq data with data and analysis results visualization through UCSC Genome Browser.

      ****************************************************

-------------------------------------------------------------------
updated: 8/15/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.0.3:

      bio/RAxML-7.0.3
      ****************************************************

       This module sets up the environment for:

       RAxML 7.0.3
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/RAxML-7.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/03/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.2.6:

      bio/RAxML-7.2.6
      ****************************************************

       This module sets up the environment for:

       RAxML 7.2.6
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/RAxML-7.2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.2.6_openmpi-1.3.2_intel-11.0.083:

      bio/RAxML-7.2.6_openmpi-1.3.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       RAxML 7.2.6, MPI enabled
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/RAxML-7.2.6_openmpi-1.3.2_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.2.6_openmpi-1.6.2_intel-13.0.079:

      bio/RAxML-7.2.6_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       RAxML 7.2.6, MPI enabled
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. This module has been built by Plamen G. Krastev with OpenMPI 1.6.2 and Intel 13.0.079.

       Use the command:

       module display bio/RAxML-7.2.6_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.2.8-alpha:

      bio/RAxML-7.2.8-alpha
      ****************************************************

       This module sets up the environment for:

       RAxML 7.2.8 ALPHA, MPI enabled
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/RAxML-7.2.8-alpha

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.3.0:

      bio/RAxML-7.3.0
      ****************************************************

       This module sets up the environment for:

       RAxML version 7.3.0
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/RAxML-7.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.3.0_openmpi-1.6.2_gcc-4.7.2:

      bio/RAxML-7.3.0_openmpi-1.6.2_gcc-4.7.2
      ****************************************************

       This module sets up the environment for:

       RAxML version 7.3.0
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/RAxML-7.3.0_openmpi-1.6.2_gcc-4.7.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.3.9:

      bio/RAxML-7.3.9
      ****************************************************

       This module sets up the environment for:

       RAxML version 7.3.9
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/RAxML-7.3.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-7.4.9:

      bio/RAxML-7.4.9
      ****************************************************

       This module sets up the environment for:

       RAxML version 7.4.9
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/RAxML-7.4.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-Light-1.0.1:

      bio/RAxML-Light-1.0.1
      ****************************************************

       This module sets up the environment for:

       RAxML-Light v1.0.1
       RAxML-Light is a stripped down RAxML version for conducting tree searches on very large trees under the CAT approximation of rate heterogeneity.

       Use the command:

       module display bio/RAxML-Light-1.0.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-Light-1.0.3:

      bio/RAxML-Light-1.0.3
      ****************************************************

       This module sets up the environment for:

       RAxML-Light v1.0.3
       RAxML-Light is a stripped down RAxML version for conducting tree searches on very large trees under the CAT approximation of rate heterogeneity.

       Use the command:

       module display bio/RAxML-Light-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/27/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RAxML-Light-1.0.5-ib:

      bio/RAxML-Light-1.0.5-ib
      ****************************************************

       This module sets up the environment for:

       RAxML-Light v1.0.5
       RAxML-Light is a stripped down RAxML version for conducting tree searches on very large trees under the CAT approximation of rate heterogeneity.

       Use the command:

       module display bio/RAxML-Light-1.0.5-ib

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/08/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RNA-pipeline-0.4.0:

      bio/RNA-pipeline-0.4.0
      ****************************************************

       This module sets up the environment for:

       RNA2MAP version 0.4.0
       RNA Analysis Tool

       Use the command:

       module display bio/RNA-pipeline-0.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/RNA-pipeline-0.5.0:

      bio/RNA-pipeline-0.5.0
      ****************************************************

       This module sets up the environment for:

       RNA2MAP version 0.5.0
       RNA Analysis Tool

       Use the command:

       module display bio/RNA-pipeline-0.5.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/09/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/SATe-20100924:

      bio/SATe-20100924
      ****************************************************

       This module sets up the environment for:

       SATe 2010-09-24
       Simultaneous Alignment and Tree Estimation

       Use the command:

       module display bio/SATe-20100924

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/21/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/SGA:

      bio/SGA
      ****************************************************

       This module sets up the environment for:

       SGA
       a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/SGA

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/SHRiMP-1.3.1:

      bio/SHRiMP-1.3.1
      ****************************************************

       This module sets up the environment for:

       SHRiMP version 1.3.1
       SHRiMP is a software package for aligning genomic reads against a target genome

       Use the command:

       module display bio/SHRiMP-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/17/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/SNAPP-1.1.1:

      bio/SNAPP-1.1.1
      ****************************************************

       This module sets up the environment for:

       SNAPP version 1.1.1
       Implementation of an MCMC based method for inferring species (population) trees and demographics from unlinked SNP data.

       Use the command:

       module display bio/SNAPP-1.1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/SOAPdenovo-Trans:

      bio/SOAPdenovo-Trans
      ****************************************************

       This module sets up the environment for:

       SOAPdenovo-Trans version 1.01, 12-22-2011
       SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.

       Use the command:

       module display bio/SOAPdenovo-Trans

       to see exactly what this module does.
less /n/sw/SOAPdenovo-Trans/example/SOAPdenovo-Trans.sh
      ****************************************************

-------------------------------------------------------------------
updated: 2/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/TGICL-2.1:

      bio/TGICL-2.1
      ****************************************************

       This module sets up the environment for:

       TGICL, version 2.1
       A software solution for clustering large EST/mRNAs datasets.

       Use the command:

       module display bio/TGICL-2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/Trimmomatic-0.27:

      bio/Trimmomatic-0.27
      ****************************************************

       This module sets up the environment for:

       Trimmomatic, version 0.27
       performs a variety of useful trimming tasks for illumina paired-end and single ended data. The selection of trimming steps and their associated parameters are supplied on the command line.

       Use the command:

       module display bio/Trimmomatic-0.27

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 4/12/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/UEA-sRNA:

      bio/UEA-sRNA
      ****************************************************

       This module sets up the environment for:

       UEA sRNA ToolKit
       Toolkit for processing the large amount of sequences obtained from high through-put experiments

       Use the command:

       module display bio/UEA-sRNA

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/27/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ViennaRNA-1.8.3:

      bio/ViennaRNA-1.8.3
      ****************************************************

       This module sets up the environment for:

       The Vienna RNA Package
       RNA Secondary Structure Prediction and Comparison

       Use the command:

       module display bio/ViennaRNA-1.8.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/01/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/XXmotif:

      bio/XXmotif
      ****************************************************

       This module sets up the environment for:

       XXmotif
       The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/XXmotif

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/31/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/YASRA:

      bio/YASRA
      ****************************************************

       This module sets up the environment for:

       YASRA ( 9 Aug 2010 )
       YASRA

       Use the command:

       module display bio/YASRA

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.2.7:

      bio/abyss-1.2.7
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.2.7
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

       Use the command:

       module display bio/abyss-1.2.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.3.0:

      bio/abyss-1.3.0
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.3.0
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. This module was built by Plamen G. Krastev

       Use the command:

       module display bio/abyss-1.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.3.2:

      bio/abyss-1.3.2
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.3.2
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. This module was built by Mike Ethier, and ABySS 1.3.2 includes google sparsehash-1.11

       Use the command:

       module display bio/abyss-1.3.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/15/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.3.2-kmer-96:

      bio/abyss-1.3.2-kmer-96
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.3.2 with kmer=96
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. This module was built by Mike Ethier, and ABySS 1.3.2 includes google sparsehash-1.11

       Use the command:

       module display bio/abyss-1.3.2-kmer-96

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.3.3-kmer-96:

      bio/abyss-1.3.3-kmer-96
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.3.3 with kmer=96
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/abyss-1.3.3-kmer-96

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/14/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/abyss-1.3.4-kmer-96:

      bio/abyss-1.3.4-kmer-96
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.3.4 with kmer=96
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

       Use the command:

       module display bio/abyss-1.3.4-kmer-96

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/agalma-0.1:

      bio/agalma-0.1
      ****************************************************

       This module sets up the environment for:

       agalma-0.1 Pipeline v0.1
       Agalma is an automated pipeline for assembling and analyzing transcriptone data. It provides rich diagnostics, including the insert size distribution of paired end data, fraction of reads that are rRNA, and the distribution of sequencing effort across genes. These diagnostics can by summarized as html reports

       Use the command:

       module display bio/agalma-0.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/agalma-0.3.0:

      bio/agalma-0.3.0
      ****************************************************

       This module sets up the environment for:

       biolite v0.3.0
       a set of analysis pipelines for transcriptome assembly (paired-end Illumina data) and phylogenetic analysis

       Use the command:

       module display bio/agalma-0.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/agalma-0.3.1:

      bio/agalma-0.3.1
      ****************************************************

       This module sets up the environment for:

       biolite v0.3.0
       a set of analysis pipelines for transcriptome assembly (paired-end Illumina data) and phylogenetic analysis

       Use the command:

       module display bio/agalma-0.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/allpathslg-35526:

      bio/allpathslg-35526
      ****************************************************

       This module sets up the environment for:

       allpathslg version 35526
       Genome Sequencing and Analysis Program - Broad Institute of MIT

       Use the command:

       module display bio/allpathslg-35526

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/allpathslg-43019:

      bio/allpathslg-43019
      ****************************************************

       This module sets up the environment for:

       allpathslg version 43019
       Genome Sequencing and Analysis Program - Broad Institute of MIT. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/allpathslg-43019

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/amber10:

      bio/amber10
      ****************************************************

       This module sets up the environment for:

       Amber
       Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules

       Use the command:

       module display bio/amber10

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/amos-3.1.0:

      bio/amos-3.1.0
      ****************************************************

       This module sets up the environment for:

       AMOS version 3.1.0
       open-source whole genome assembly software. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/amos-3.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ampliconnoise-1.21:

      bio/ampliconnoise-1.21
      ****************************************************

       This module sets up the environment for:

       AmpliconNoise, Version 1.21
       AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.

       Use the command:

       module display bio/ampliconnoise-1.21

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 9/03/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ampliconnoise-1.27:

      bio/ampliconnoise-1.27
      ****************************************************

       This module sets up the environment for:

       AmpliconNoise, Version 1.27
       AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. This module has been built by Plamen G. Krastev

       Use the command:

       module display bio/ampliconnoise-1.27

       to see exactly what this module does.

       This module was built by:

       pkrastev

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/analysis-0.8.1:

      bio/analysis-0.8.1
      ****************************************************

       This module sets up the environment for:

       analysis version 0.8.1
       C++ software for evolutionary genetic analysis. This module has been bult by Plamen G. Krastev.

       Use the command:

       module display bio/analysis-0.8.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/antismash-1.2.0:

      bio/antismash-1.2.0
      ****************************************************

       This module sets up the environment for:

       antismash version 1.2.0
       antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier

       Use the command:

       module display bio/antismash-1.2.0

       to see exactly what this module does.
run by :java jvm-args -jar /n/sw/antismash-1.2.0/antismash.jar
JVM argument -Xmx2g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/arb-5.1:

      bio/arb-5.1
      ****************************************************

       This module sets up the environment for:

       ARB Version 5.1
       A software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction.

       Use the command:

       module display bio/arb-5.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/24/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/autodock_vina-1.1.2:

      bio/autodock_vina-1.1.2
      ****************************************************

       This module sets up the environment for:

       autodock-vina version 1.1.2
       a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/autodock_vina-1.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/autodocksuite-4.2.5.1:

      bio/autodocksuite-4.2.5.1
      ****************************************************

       This module sets up the environment for:

       autodocksuite version 4.2.5.1
       a suite of automated docking tools. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/autodocksuite-4.2.5.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bam2fastq-1.1.0:

      bio/bam2fastq-1.1.0
      ****************************************************

       This module sets up the environment for:

       bam2fastq
       a tool to extract raw sequences (with qualities). Primarily useful to those wishing to duplicate or extend previous analyses. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bam2fastq-1.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bamtools-1.0.2:

      bio/bamtools-1.0.2
      ****************************************************

       This module sets up the environment for:

       BAMTOOLS version 1.0.2
       BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bamtools-1.0.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bamtools-2.2.0:

      bio/bamtools-2.2.0
      ****************************************************

       This module sets up the environment for:

       BAMTOOLS version 2.2.0
       BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bamtools-2.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bamutil-1.0.2:

      bio/bamutil-1.0.2
      ****************************************************

       This module sets up the environment for:

       bamUtil
       a repository that contains several programs that perform operations on SAM/BAM files. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bamutil-1.0.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bamutil-1.0.6:

      bio/bamutil-1.0.6
      ****************************************************

       This module sets up the environment for:

       bamUtil version 1.0.6
       a repository that contains several programs that perform operations on SAM/BAM files. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bamutil-1.0.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/17/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bayessc-1.0:

      bio/bayessc-1.0
      ****************************************************

       This module sets up the environment for:

       BayeSSC, version 1.0
       Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0

       Use the command:

       module display bio/bayessc-1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bayessc-1.0_mod:

      bio/bayessc-1.0_mod
      ****************************************************

       This module sets up the environment for:

       BayeSSC, version 1.0
       Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bayessc-1.0_mod

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bcl2fastq-1.8.3:

      bio/bcl2fastq-1.8.3
      ****************************************************

       This module sets up the environment for:

       bcl2fastq version 1.8.3
       Tool to handle bcl conversion and demultiplexing of both unzipped and zipped bcl files. Built by Mike Ethier

       Use the command:

       module display bio/bcl2fastq-1.8.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/02/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/beagle-lib-2011-10-11:

      bio/beagle-lib-2011-10-11
      ****************************************************

       This module sets up the environment for:

       BEAGLE, svn checkout October 11, 2011
       a general purpose library for evaluating the likelihood of sequence evolution on trees

       Use the command:

       module display bio/beagle-lib-2011-10-11

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 10/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/beast-1.5.3:

      bio/beast-1.5.3
      ****************************************************

       This module sets up the environment for:

       BEAST version 1.5.3
       Bayesian Evolutionary Analysis Sampling Trees

       Use the command:

       module display bio/beast-1.5.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/22/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/beast-1.7.1:

      bio/beast-1.7.1
      ****************************************************

       This module sets up the environment for:

       BEAST version 1.7.1
       Bayesian Evolutionary Analysis Sampling Trees. This module was built by Plamen G Krastev.

       Use the command:

       module display bio/beast-1.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/beast-1.7.5:

      bio/beast-1.7.5
      ****************************************************

       This module sets up the environment for:

       BEAST version 1.7.5
       Bayesian Evolutionary Analysis Sampling Trees. This module was built by Plamen G Krastev.

       Use the command:

       module display bio/beast-1.7.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/best-2.3.1_openmpi-1.3.3_intel-11.1.046:

      bio/best-2.3.1_openmpi-1.3.3_intel-11.1.046
      ****************************************************

       This module sets up the environment for:

       BEST version 3.2 with MPI support
       Bayesian Estimation of Species Trees

       Use the command:

       module display bio/best-2.3.1_openmpi-1.3.3_intel-11.1.046

       to see exactly what this module does.

       This build includes patches described at
       http://www.bestgrid.org/index.php/Bioinformatics_applications_at_University_of_Canterbury_HPC#Installing_MrBayes
       o fix for problem with SumP hanging in MPI on error
       o fix minor issue in mcmcdiagn param print
       o fix for 64-bit architecture
       plus a custom FAS IT RC patch
       o fix to not use readline when stdin is not a tty


      ****************************************************

-------------------------------------------------------------------
updated: 12/23/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bfast-0.6.4e:

      bio/bfast-0.6.4e
      ****************************************************

       This module sets up the environment for:

       BFAST version 0.6.4e
       Blat-like Fast Accurate Search Tool

       Use the command:

       module display bio/bfast-0.6.4e

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bimbam-1.0:

      bio/bimbam-1.0
      ****************************************************

       This module sets up the environment for:

       BIMBAM version 1.0
       BIMBAM implements methods for Bayesian IMputation-Based Association Mapping.

       Use the command:

       module display bio/bimbam-1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bio++2.0:

      bio/bio++2.0
      ****************************************************

       This module sets up the environment for:

       bio++, version 2.0.0
       bio++2.0 suite

       Use the command:

       module display bio/bio++2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biolite-0.3.0:

      bio/biolite-0.3.0
      ****************************************************

       This module sets up the environment for:

       biolite v0.3.0
       a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines.

       Use the command:

       module display bio/biolite-0.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biolite-0.3.0_python-2.7.3:

      bio/biolite-0.3.0_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       biolite version 0.3.0
       a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/biolite-0.3.0_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biolite-0.3.1_python-2.7.3:

      bio/biolite-0.3.1_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       biolite version 0.3.1
       a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines. This module has been built with Python 2.7.3 by Mike Ethier.

       Use the command:

       module display bio/biolite-0.3.1_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biom-format-0.9.3:

      bio/biom-format-0.9.3
      ****************************************************

       This module sets up the environment for:

       Biom Format version 0.9.3
       software tools for working with BIOM-formatted files and the tables they represent. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/biom-format-0.9.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biom-format-1.0.0:

      bio/biom-format-1.0.0
      ****************************************************

       This module sets up the environment for:

       Biom Format version 1.0.0
       software tools for working with BIOM-formatted files and the tables they represent. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/biom-format-1.0.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/biom-format-1.1.1_python-2.7.3:

      bio/biom-format-1.1.1_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       Biom Format version 1.1.1
       software tools for working with BIOM-formatted files and the tables they represent. This module has been built with Python 2.7.3 by Plamen G Krastev.

       Use the command:

       module display bio/biom-format-1.1.1_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/blast-2.2.22:

      bio/blast-2.2.22
      ****************************************************

       This module sets up the environment for:

       blast version 2.2.22
       Set up environment for NCBI blast. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/blast-2.2.22

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/blast2go:

      bio/blast2go
      ****************************************************

       This module sets up the environment for:

       Blast2GO (B2G) Pipeline Version (B2G4Pipe),version 2.3.5
       B2G is an GO annotation and functional analysis systems based on sequence similarity (Blast)

       Use the command:

       module display bio/blast2go

       to see exactly what this module does.
run by :java -Xmx2g -jar /n/sw/blast2go/blast2go.jar -prop /n/sw/blast2go/b2gPipe.properties -in /n/sw/blast2go/blastResult_2009.xml -v -a -out MyAnnot
JVM argument -Xmx2g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 6/08/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/blast2go-2.5.0:

      bio/blast2go-2.5.0
      ****************************************************

       This module sets up the environment for:

       Blast2GO (B2G) Pipeline Version (B2G4Pipe),version 2.5.0
       B2G is a GO annotation and functional analysis program based on sequence similarity (Blast).
Here is the format of an example command that can be used with this Blast2GO installation:
java -cp /n/sw/blast2go-2.5.0/b2g4pipe/*:/n/sw/blast2go-2.5.0/b2g4pipe/ext/*: es.blast2go.prog.B2GAnnotPipe -in <blast_results.xml> -out <output_name> -prop /n/sw/blast2go-2.5.0/b2g4pipe/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex -goslim

       Use the command:

       module display bio/blast2go-2.5.0

       to see exactly what this module does.
run by :java -Xmx2g -jar /n/sw/blast2go-2.5.0/b2g4pipe/blast2go.jar -prop /n/sw/blast2go-2.5.0/b2g4pipe/b2gPipe.properties -in /n/sw/blast2go-2.5.0/b2g4pipe/10_BlastResults_2011.xml -v -a -out MyAnnot
JVM argument -Xmx2g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 5/03/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/blastz-2004-12-27:

      bio/blastz-2004-12-27
      ****************************************************

       This module sets up the environment for:

       BLASTZ version 2004-12-27
       BLASTZ alignment programs (obsolete; replaced by LASTZ)

       Use the command:

       module display bio/blastz-2004-12-27

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 5/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie-0.11.3:

      bio/bowtie-0.11.3
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 0.11.3
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie-0.11.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/07/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie-0.12.7:

      bio/bowtie-0.12.7
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 0.12.7
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie-0.12.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/06/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie-0.12.9:

      bio/bowtie-0.12.9
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 0.12.9
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie-0.12.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie2-2.0.0-beta5:

      bio/bowtie2-2.0.0-beta5
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 2-2.0.0-beta5
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie2-2.0.0-beta5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie2-2.0.0-beta6:

      bio/bowtie2-2.0.0-beta6
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 2-2.0.0-beta6
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie2-2.0.0-beta6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie2-2.0.0-beta7:

      bio/bowtie2-2.0.0-beta7
      ****************************************************

       This module sets up the environment for:

       Bowtie Version 2-2.0.0-beta7
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/bowtie2-2.0.0-beta7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/30/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bowtie2-2.0.5:

      bio/bowtie2-2.0.5
      ****************************************************

       This module sets up the environment for:

       Bowtie 2 Version 2.0.5
       Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. It supports gapped, local, and paired-end alignment modes, and outputs alignments in SAM format.

       Use the command:

       module display bio/bowtie2-2.0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/23/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bpp-core-2.0.0:

      bio/bpp-core-2.0.0
      ****************************************************

       This module sets up the environment for:

       bpp-core, version 2.0.0
       C++ libraries for Bioinformatics.

       Use the command:

       module display bio/bpp-core-2.0.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bpp-utils-1.5.0:

      bio/bpp-utils-1.5.0
      ****************************************************

       This module sets up the environment for:

       bpp-utils, version 1.5.0
       bpp-utils-1.5.0

       Use the command:

       module display bio/bpp-utils-1.5.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/breseq-0.14:

      bio/breseq-0.14
      ****************************************************

       This module sets up the environment for:

       breseq, version 0.14
       breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.

       Use the command:

       module display bio/breseq-0.14

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 9/24/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/breseq-0.18:

      bio/breseq-0.18
      ****************************************************

       This module sets up the environment for:

       breseq, version 0.18
       breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.

       Use the command:

       module display bio/breseq-0.18

       to see exactly what this module does.

       This module was built by:

       Plamen G. Krastev

      ****************************************************

-------------------------------------------------------------------
updated: 10/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/breseq-0.20:

      bio/breseq-0.20
      ****************************************************

       This module sets up the environment for:

       breseq, version 0.20
       breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.

       Use the command:

       module display bio/breseq-0.20

       to see exactly what this module does.

       This module was built by:

       Plamen G. Krastev

      ****************************************************

-------------------------------------------------------------------
updated: 10/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/breseq-0.21:

      bio/breseq-0.21
      ****************************************************

       This module sets up the environment for:

       breseq, version 0.21
       breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.

       Use the command:

       module display bio/breseq-0.21

       to see exactly what this module does.

       This module was built by:

       Plamen G. Krastev

      ****************************************************

-------------------------------------------------------------------
updated: 12/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bsmap-2.6:

      bio/bsmap-2.6
      ****************************************************

       This module sets up the environment for:

       bsmap version 2.6
       BSMAP is a short reads mapping program for bisulfite sequencing in DNA methylation study. Bisulfite treatment coupled with next generation sequencing could estimate the methylation ratio of every single Cytosine location in the genome by mapping high throughput bisulfite reads to the reference sequences.

       Use the command:

       module display bio/bsmap-2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/19/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bucky-1.3.1:

      bio/bucky-1.3.1
      ****************************************************

       This module sets up the environment for:

       BUCKy version 1.3.1
       BUCKy is a free program to combine molecular data from multiple loci.

       Use the command:

       module display bio/bucky-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/22/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bwa-0.5.9:

      bio/bwa-0.5.9
      ****************************************************

       This module sets up the environment for:

       Burrows-Wheeler Aligner - bwa:version 0.5.9
       Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

       Use the command:

       module display bio/bwa-0.5.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bwa-0.6.2:

      bio/bwa-0.6.2
      ****************************************************

       This module sets up the environment for:

       Burrows-Wheeler Aligner - bwa:version 0.6.2
       Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/bwa-0.6.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/bwa-0.7.4:

      bio/bwa-0.7.4
      ****************************************************

       This module sets up the environment for:

       Burrows-Wheeler Aligner - bwa:version 0.7.4
       Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. This module has been built by Mike Ethier.

       Use the command:

       module display bio/bwa-0.7.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cd-hit-3.1:

      bio/cd-hit-3.1
      ****************************************************

       This module sets up the environment for:

       cd-hit, version 3.1
       CD-HIT is a program for clustering large protein database at high sequence identity threshold.

       Use the command:

       module display bio/cd-hit-3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cd-hit-v4.6-2012-04-25:

      bio/cd-hit-v4.6-2012-04-25
      ****************************************************

       This module sets up the environment for:

       cd-hit, version 4.6
       CD-HIT is a program for clustering large protein database at high sequence identity threshold.

       Use the command:

       module display bio/cd-hit-v4.6-2012-04-25

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/27/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cdbfasta:

      bio/cdbfasta
      ****************************************************

       This module sets up the environment for:

       cdbfasta
       Fast indexing/retrieval of fasta records from flat file databases

       Use the command:

       module display bio/cdbfasta

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/chimeraslayer-2010-04-29:

      bio/chimeraslayer-2010-04-29
      ****************************************************

       This module sets up the environment for:

       ChimeraSlayer, version 2010-04-29
       A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

       Use the command:

       module display bio/chimeraslayer-2010-04-29

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/circos-0.62:

      bio/circos-0.62
      ****************************************************

       This module sets up the environment for:

       Circos version 0.62
       a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/circos-0.62

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/clearcut-1.0.9:

      bio/clearcut-1.0.9
      ****************************************************

       This module sets up the environment for:

       Clearcut, version 1.0.9
       Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of
Idaho.

       Use the command:

       module display bio/clearcut-1.0.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/clustal-omega-1.0.3:

      bio/clustal-omega-1.0.3
      ****************************************************

       This module sets up the environment for:

       clustal-omega-1.0.3, version 1.0.3
       Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.

       Use the command:

       module display bio/clustal-omega-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/clustalw-1.81:

      bio/clustalw-1.81
      ****************************************************

       This module sets up the environment for:

       clustalw, version 1.81
       Multiple alignment of nucleic acid and protein sequences

       Use the command:

       module display bio/clustalw-1.81

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/clustalw-2.0.12:

      bio/clustalw-2.0.12
      ****************************************************

       This module sets up the environment for:

       clustalw, version 2.0.12
       Multiple alignment of nucleic acid and protein sequences

       Use the command:

       module display bio/clustalw-2.0.12

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/concaterpillar-1.4:

      bio/concaterpillar-1.4
      ****************************************************

       This module sets up the environment for:

       Concaterpillar V1.4
       A hierarchical likelihood ratio test for phylogenetic congruence. http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#Concaterpillar

       Use the command:

       module display bio/concaterpillar-1.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/05/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/consed-19.0:

      bio/consed-19.0
      ****************************************************

       This module sets up the environment for:

       consed version 19.0
       consed is a program for viewing and editing assemblies. It is the finishing part of the Phred/Phrap/Consed package

       Use the command:

       module display bio/consed-19.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/21/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/correction:

      bio/correction
      ****************************************************

       This module sets up the environment for:

       correction for SOAPdenovo
       The read correction package is a short-read correction tool and part of SOAPdenovo . It is specially designed to correct Illum ina GA short reads

       Use the command:

       module display bio/correction

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cortex-1.0.5.15:

      bio/cortex-1.0.5.15
      ****************************************************

       This module sets up the environment for:

       cortex version 1.0.5.15
       A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/cortex-1.0.5.15

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cortex_var_1.0.5.3:

      bio/cortex_var_1.0.5.3
      ****************************************************

       This module sets up the environment for:

       cortex_var_1.0.5.3
       A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/cortex_var_1.0.5.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cpat-1.2.1_python-2.7.3:

      bio/cpat-1.2.1_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       CPAT version 1.2.1
       program to discriminate coding and noncoding genes using logistic regression model based on 4 selected features. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/cpat-1.2.1_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/crux-1.2.0:

      bio/crux-1.2.0
      ****************************************************

       This module sets up the environment for:

       Crux version 1.2.0
       Crux is a software toolkit for molecular phylogenetic inference that runs on (at least) Linux, FreeBSD, and Mac OS X. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/crux-1.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/21/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/crux-1.2.0_mpi4py-1.3:

      bio/crux-1.2.0_mpi4py-1.3
      ****************************************************

       This module sets up the environment for:

       Crux version 1.2.0
       Crux is a software toolkit for molecular phylogenetic inference that runs on (at least) Linux, FreeBSD, and Mac OS X. This module has been built with mpi4py version 1.3 by Plamen G. Krastev.

       Use the command:

       module display bio/crux-1.2.0_mpi4py-1.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/22/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/csblast-2.1.0-linux64:

      csblast-2.1.0-linux64 module
      ****************************************************

       This module sets up the following environment
       variables for csblast-2.1.0-linux64:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 7/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-0.8.0:

      bio/cufflinks-0.8.0
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 0.8.0
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

       Use the command:

       module display bio/cufflinks-0.8.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-0.9.3:

      bio/cufflinks-0.9.3
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 0.9.3
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

       Use the command:

       module display bio/cufflinks-0.9.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-1.1.0:

      bio/cufflinks-1.1.0
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 1.1.0
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

       Use the command:

       module display bio/cufflinks-1.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-2.0.1.Linux_x86_64:

      bio/cufflinks-2.0.1.Linux_x86_64
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 2.0.1
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

       Use the command:

       module display bio/cufflinks-2.0.1.Linux_x86_64

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-2.0.2.Linux_x86_64:

      bio/cufflinks-2.0.2.Linux_x86_64
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 2.0.2 (BETA)
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

2.0.2 release - 7/8/2012
This release fixes several bugs:
Some users were experience a crash on exit in Cufflinks when run with bias correction. The source of the crash has been fixed.
A few minor fixes in the estimation routines for cross-replicate variability.
Providing the same BAM file multiple times was producing inconsistent expression values. This has been corrected.

       Use the command:

       module display bio/cufflinks-2.0.2.Linux_x86_64

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cufflinks-2.1.1.Linux_x86_64:

      bio/cufflinks-2.1.1.Linux_x86_64
      ****************************************************

       This module sets up the environment for:

       Cufflinks Version 2.1.1
       Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. This module has been built by Plamen G. Krastev

       Use the command:

       module display bio/cufflinks-2.1.1.Linux_x86_64

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cutadapt-1.0:

      bio/cutadapt-1.0
      ****************************************************

       This module sets up the environment for:

       cutadapt 1.0
       A tool that removes adapter sequences from DNA sequencing reads

       Use the command:

       module display bio/cutadapt-1.0

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 5/30/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cutadapt-1.2.1:

      bio/cutadapt-1.2.1
      ****************************************************

       This module sets up the environment for:

       cutadapt 1.2.1
       cutadapt removes adapter sequences from DNA high-throughput sequencing data. It is implemented in Python, with an extension module, written in C, that implements the alignment algorithm.

       Use the command:

       module display bio/cutadapt-1.2.1

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 1/24/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cyana-2.1:

      bio/cyana-2.1
      ****************************************************

       This module sets up the environment for:

       CYANA version 2.1
       Combined assignment and dynamics algorithm for NMR applications (CYANA) is a program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

       Use the command:

       module display bio/cyana-2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/29/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/cytoscape-v2.7.0:

      bio/cytoscape-v2.7.0
      ****************************************************

       This module sets up the environment for:

       cytoscape version 2.7.0
       an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/cytoscape-v2.7.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/dadi:

      bio/dadi
      ****************************************************

       This module sets up the environment for:

       dadi, Diffusion Approximation for Demographic Inference
       dadi implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum. One of dadi's main benefits is speed: fitting a two-population model typically takes around 10 minutes, and run time is independent of the number of SNPs in your data set. dadi is also flexible, handling up to three simultaneous populations, with arbitrary timecourses for population size and migration, plus the possibility of admixture and population-specific selection.

       Use the command:

       module display bio/dadi

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/dendropy-3.12.0_python-2.7.1:

      bio/dendropy-3.12.0_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       DendroPy version 3.12.0
       a Python library for phylogenetic computing. This module has been built with Python version 2.7.1 by Plamen G Krastev.

       Use the command:

       module display bio/dendropy-3.12.0_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/28/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/denoiser-0.84:

      bio/denoiser-0.84
      ****************************************************

       This module sets up the environment for:

       Denoiser, version 0.84
       Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

       Use the command:

       module display bio/denoiser-0.84

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/dindel-1.01:

      bio/dindel-1.01
      ****************************************************

       This module sets up the environment for:

       Dindel version 1.01
       a program for calling small indels from short-read sequence data ('next generation sequence data'). It is currently designed to handle only Illumina data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/dindel-1.01

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/dnaclust:

      bio/dnaclust
      ****************************************************

       This module sets up the environment for:

       DNACLUST
       DNACLUST is a tool for clustering millions of short DNA sequences.

       Use the command:

       module display bio/dnaclust

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 4/07/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eigensoft-3.0:

      bio/eigensoft-3.0
      ****************************************************

       This module sets up the environment for:

       EIGENSOFT version 3.0, built with Gnu compilers
       See http://genepath.med.harvard.edu/~reich/Software.htm for description of capabilities

       Use the command:

       module display bio/eigensoft-3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/04/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eigensoft-4.2:

      bio/eigensoft-4.2
      ****************************************************

       This module sets up the environment for:

       EIGENSOFT version 4.2, built with GNU version 4.1.2 compilers
       Please see http://genepath.med.harvard.edu/~reich/Software.htm for detailed description of capabilities. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/eigensoft-4.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-1.9:

      bio/eman-1.9
      ****************************************************

       This module sets up the environment for:

       EMAN version 1.9
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community

       Use the command:

       module display bio/eman-1.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/17/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-2.0.3:

      bio/eman-2.0.3
      ****************************************************

       This module sets up the environment for:

       EMAN version 2.0.3
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community

       Use the command:

       module display bio/eman-2.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-2.0.4:

      bio/eman-2.0.4
      ****************************************************

       This module sets up the environment for:

       EMAN version 2.04
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/eman-2.0.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-2.0.4_mvapich2-1.5:

      bio/eman-2.0.4_mvapich2-1.5
      ****************************************************

       This module sets up the environment for:

       EMAN version 2.04
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community. This module has been built with Mvapich2 version 1.5 and GCC version 4.3.3 by Plamen G. Krastev.

       Use the command:

       module display bio/eman-2.0.4_mvapich2-1.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-2.0.5_mvapich2-1.5:

      bio/eman-2.0.5_mvapich2-1.5
      ****************************************************

       This module sets up the environment for:

       EMAN version 2.05
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community. This module has been built with Mvapich2 version 1.5 and GCC version 4.3.3 by Plamen G. Krastev.

       Use the command:

       module display bio/eman-2.0.5_mvapich2-1.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-2.0.6_mvapich2-1.5:

      bio/eman-2.0.6_mvapich2-1.5
      ****************************************************

       This module sets up the environment for:

       EMAN version 2.06
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community. This module has been built with Mvapich2 version 1.5 and GCC version 4.3.3 by Plamen G. Krastev.

       Use the command:

       module display bio/eman-2.0.6_mvapich2-1.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/17/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/eman-x86_64-gcc4_9-30-2011:

      bio/eman-x86_64-gcc4_9-30-2011
      ****************************************************

       This module sets up the environment for:

       EMAN version x86_64-gcc4-2.0RC4
       EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community

       Use the command:

       module display bio/eman-x86_64-gcc4_9-30-2011

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/12/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/estscan-3.0.3:

      bio/estscan-3.0.3
      ****************************************************

       This module sets up the environment for:

       estscan version 3.0.3
       ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.

       Use the command:

       module display bio/estscan-3.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/22/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ete2a1_python-2.7.1:

      bio/ete2a1_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       ETE2
       ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/ete2a1_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/18/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/euler-sr.1.1.2:

      bio/euler-sr.1.1.2
      ****************************************************

       This module sets up the environment for:

       euler-sr 1.1.2 ( 9 Aug 2010 )
       EULER-SR is a program for de novo assembly of reads

       Use the command:

       module display bio/euler-sr.1.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/12/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/express-1.3.1:

      bio/express-1.3.1
      ****************************************************

       This module sets up the environment for:

       express version eersion 1.3.1
       Streaming quantification for high-throughput sequencing. This module has been built by Mike Ethier

       Use the command:

       module display bio/express-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fast:

      fast-linux-64 module
      ****************************************************

       This module sets up the following environment
       variables for fast-linux-64:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 7/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fasta-35.4.11:

      bio/fasta-35.4.11
      ****************************************************

       This module sets up the environment for:

       FASTA version 35.4.11
       from UVa

       Use the command:

       module display bio/fasta-35.4.11

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fasthmm-1.3.1:

      bio/fasthmm-1.3.1
      ****************************************************

       This module sets up the environment for:

       FastHMM and FastBLAST
       Tools for Analyzing Large Protein Sequence Databases

       Use the command:

       module display bio/fasthmm-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/31/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fastphase.1.3.0-gnu:

      bio/fastphase.1.3.0-gnu
      ****************************************************

       This module sets up the environment for:

       fastPHASE v.1.3.0
       fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data

       Use the command:

       module display bio/fastphase.1.3.0-gnu

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/10/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fastphase.1.3.0-intel-11.0.083:

      bio/fastphase.1.3.0-intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       fastPHASE v.1.3.0
       fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data

       Use the command:

       module display bio/fastphase.1.3.0-intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/10/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fastqc-0.10.0:

      bio/fastqc-0.10.0
      ****************************************************

       This module sets up the environment for:

       FastQC, version 0.10.0
       a quality control tool for high throughput sequence data

       Use the command:

       module display bio/fastqc-0.10.0

       to see exactly what this module does.

       This module was built by:

       john_brunelle@harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 10/03/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fasttree-2.1.0:

      bio/fasttree-2.1.0
      ****************************************************

       This module sets up the environment for:

       FastTree version 2.1.0
       FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

       Use the command:

       module display bio/fasttree-2.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fasttree-2.1.3:

      bio/fasttree-2.1.3
      ****************************************************

       This module sets up the environment for:

       FastTree version 2.1.3
       FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

       Use the command:

       module display bio/fasttree-2.1.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fasttree-2.1.4:

      bio/fasttree-2.1.4
      ****************************************************

       This module sets up the environment for:

       FastTree version 2.1.4
       FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

       Use the command:

       module display bio/fasttree-2.1.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/fastx_toolkit-0.0.13:

      bio/fastx_toolkit-0.0.13
      ****************************************************

       This module sets up the environment for:

       FASTX-Toolkit version 0.0.13
       The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

       Use the command:

       module display bio/fastx_toolkit-0.0.13

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/frealign-8.09:

      bio/frealign-8.09
      ****************************************************

       This module sets up the environment for:

       Frealign version 8.09_111001
       a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles

       Use the command:

       module display bio/frealign-8.09

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 4/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/gapcloser-1.12:

      bio/gapcloser-1.12
      ****************************************************

       This module sets up the environment for:

       GapCloser v1.12
       The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, using the abundant pair relationships of short reads.

       Use the command:

       module display bio/gapcloser-1.12

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/gcta_1.13:

      bio/gcta_1.13
      ****************************************************

       This module sets up the environment for:

       gcta version 1.13
       GCTA is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits. Built by Mike Ethier

       Use the command:

       module display bio/gcta_1.13

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/04/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/gimsan_cmdline-5.7.2013:

      bio/gimsan_cmdline-5.7.2013
      ****************************************************

       This module sets up the environment for:

       gimsan_cmdline - GIMSAN (GIbbsMarkov with Significance ANalysis)
       GIMSAN (GIbbsMarkov with Significance ANalysis) is a web-server tool for de novo motif discovery. Module built my Mike Ethier.

       Use the command:

       module display bio/gimsan_cmdline-5.7.2013

       to see exactly what this module does.
      ****************************************************

-------------------------------------------------------------------
updated: 5/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/glimmer3.02:

      bio/glimmer3.02
      ****************************************************

       This module sets up the environment for:

       glimmer version 3.02
       Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/glimmer3.02

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/gmap-2011-03-28.v3:

      gmap-2011-03-28.v3 module
      ****************************************************

       This module sets up the following environment
       variables for gmap-2011-03-28.v3: PATH

       Please run as (notice database location and name)

       gmap      -D '/n/bioseq/gmap_gsnap/' -d 'mm9_gmap'

       please let us know if different genome database needed.
      ****************************************************

-------------------------------------------------------------------
updated: 8/10/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/gmap-2012-06-02:

      gmap-2012-06-02 module
      ****************************************************

       This module sets up the following environment
       variables for gmap-2012-06-02: PATH

       Please run as (notice database location and name)

       gmap      -D '/n/bioseq/gmap_gsnap/' -d 'mm9_gmap'

       please let us know if different genome database needed.
      ****************************************************

-------------------------------------------------------------------
updated: 6/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/goby_1.9.8.2.1:

      bio/goby_1.9.8.2.1
      ****************************************************

       This module sets up the environment for:

       goby version 1.9.8.2.1
       Goby is a next-gen data management framework designed to facilitate the implementation of efficient data analysis pipelines.

       Use the command:

       module display bio/goby_1.9.8.2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hamster-1.2.1:

      bio/hamster-1.2.1
      ****************************************************

       This module sets up the environment for:

       hamster version 1.2.1
       HAMSTER allows users to examine the experiments of their microarray data as a set of minimum spanning trees

       Use the command:

       module display bio/hamster-1.2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hamstrsearch_local_v8b:

      bio/hamstrsearch_local_v8b
      ****************************************************

       This module sets up the environment for:

       hamstrsearch_local-hmmer3 version 8b
       HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

       Use the command:

       module display bio/hamstrsearch_local_v8b

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hmmer-2.3.2:

      bio/hmmer-2.3.2
      ****************************************************

       This module sets up the environment for:

       HMMER version 2.3.2
       profile hidden Markov models software for protein sequence analysis

       Use the command:

       module display bio/hmmer-2.3.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/29/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hmmer-3.0:

      bio/hmmer-3.0
      ****************************************************

       This module sets up the environment for:

       HMMER version 3.0
       profile hidden Markov models software for protein sequence analysis

       Use the command:

       module display bio/hmmer-3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/homer:

      bio/homer
      ****************************************************

       This module sets up the environment for:

       homer version 3.1
       a collection of Perl modules for chip-seq projects

       Use the command:

       module display bio/homer

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/31/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hpc_data_tools:

      bio/hpc_data_tools
      ****************************************************

       This module sets up the environment for:

       Harvard HPC Bio Data Tools
       Harvard Research Computing tools for munging biological data

       Use the command:

       module display bio/hpc_data_tools

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/htseq-0.5.3_python-2.7.3:

      bio/htseq-0.5.3_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       HTSeq version 0.5.3
       a Python package that provides infrastructure to process data from high-throughput sequencing assays. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/htseq-0.5.3_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hyphy_gnu-4.1.2:

      bio/hyphy_gnu-4.1.2
      ****************************************************

       This module sets up the environment for:

       HyPhy
       HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. This module was built by Plamen G. Krastev

       Use the command:

       module display bio/hyphy_gnu-4.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/hyphy_openmpi-1.4.2_gnu-4.1.2:

      bio/hyphy_openmpi-1.4.2_gnu-4.1.2
      ****************************************************

       This module sets up the environment for:

       HyPhy
       HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. This module was built by Plamen G. Krastev

       Use the command:

       module display bio/hyphy_openmpi-1.4.2_gnu-4.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/icorn-0.97:

      bio/icorn-0.97
      ****************************************************

       This module sets up the environment for:

       iCORN-v0.97
       ICORN a.k.a. ACORN is a software to correct reference genome sequences. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/icorn-0.97

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/idba-0.17:

      bio/idba-0.17
      ****************************************************

       This module sets up the environment for:

       IDBA tool kit 0.17 for 64-bit Linux
       IDBA is a open source de novo assembler for next-generation short read sequences. It is fast, parallel and capable of assembling large scale genomic assembly such as human genome. . Module built my Mike Ethier.

       Use the command:

       module display bio/idba-0.17

       to see exactly what this module does.
      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/igv-2.1.24:

      bio/igv-2.1.24
      ****************************************************

       This module sets up the environment for:

       Integrative Genomics Viewer (IGV) version 2.1.24
       a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. This module has been installed by Plamen G.Krastev.

       Use the command:

       module display bio/igv-2.1.24

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/igvtools-2.2.2:

      bio/igvtools-2.2.2
      ****************************************************

       This module sets up the environment for:

       Interactive Genomics Viewer Tools, version 2.2.2
       a high-performance visualization tool for interactive exploration of large, integrated genomic datasets

       Use the command:

       module display bio/igvtools-2.2.2

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/illumina_assembly_workflow:

      bio/illumina_assembly_workflow
      ****************************************************

       This module sets up the environment for:

       Illumina Assembly Workflow from Dunn, Andrade, et. al.
       Please site the following when using the process_oases_transcripts script:Smith S., Wilson N.G., Goetz F., Feehery C., Andrade S.C.S., Rouse G.W., Giribet G., Dunn C.D. Cracking the shell: phylogenomics and evolution of molluscs. Nature, submitted

       Use the command:

       module display bio/illumina_assembly_workflow

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/im-ima:

      bio/im-ima
      ****************************************************

       This module sets up the environment for:

       IM
       IM/IMA Isolation w/Migration model using Markov chain Monte Carlo

       Use the command:

       module display bio/im-ima

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ima2:

      bio/ima2
      ****************************************************

       This module sets up the environment for:

       IM
       IMA2 Isolation w/Migration model using Markov chain Monte Carlo

       Use the command:

       module display bio/ima2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/17/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/infernal-1.0.2:

      bio/infernal-1.0.2
      ****************************************************

       This module sets up the environment for:

       Infernal, version 1.0.2
       Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities.

       Use the command:

       module display bio/infernal-1.0.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/intarna-1.2.2:

      bio/intarna-1.2.2
      ****************************************************

       This module sets up the environment for:

       IntaRNA
       Efficient Target Prediction Incorporating Accessibility of Target Sites

       Use the command:

       module display bio/intarna-1.2.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/01/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/intersnp-1.0.10_gcc-4.6.1:

      bio/intersnp-1.0.10_gcc-4.6.1
      ****************************************************

       This module sets up the environment for:

       INTERSNP Version 1.0.10
       INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data and quantitative traits. SNPs are selected for joint analysis using a priori information. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/intersnp-1.0.10_gcc-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/30/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/intersnp-1.0.9_gcc-4.6.1:

      bio/intersnp-1.0.9_gcc-4.6.1
      ****************************************************

       This module sets up the environment for:

       INTERSNP Version 1.0.9
       INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data and quantitative traits. SNPs are selected for joint analysis using a priori information. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/intersnp-1.0.9_gcc-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/02/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ispalign:

      bio/ispalign
      ****************************************************

       This module sets up the environment for:

       ISPAlign
       A multiple sequence alignment program that automatically performs database search from each input sequence, defines an appropriate subset of intermediate sequences from among the hits, and uses a greedy strategy to select a small subset of intermediate sequences that are far away from each other to add to the input sequences

       Use the command:

       module display bio/ispalign

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/30/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/jellyfish-1.1.4_gcc-4.6.1:

      bio/jellyfish-1.1.4_gcc-4.6.1
      ****************************************************

       This module sets up the environment for:

       Jellyfish version 1.1.4
       A tool for fast, memory-efficient counting of k-mers in DNA. This module has been built with GCC 4.6.1 by Plamen G Krastev.

       Use the command:

       module display bio/jellyfish-1.1.4_gcc-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/11/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/jmodeltest0.1:

      bio/jmodeltest0.1
      ****************************************************

       This module sets up the environment for:

       jmodeltest0.1,version 0.1
       jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

       Use the command:

       module display bio/jmodeltest0.1

       to see exactly what this module does.
run by :java -Xmx2g -jar /n/sw/jmodeltest0.1/jModelTest.jar
JVM argument -Xmx2g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 4/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/lagrange:

      bio/lagrange
      ****************************************************

       This module sets up the environment for:

       Likelihood analysis of geographic range evolution
       Likelihood analysis of geographic range evolution

       Use the command:

       module display bio/lagrange

       to see exactly what this module does.



      ****************************************************

-------------------------------------------------------------------
updated: 4/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/lagrange-ad55ae9:

      bio/lagrange-ad55ae9
      ****************************************************

       This module sets up the environment for:

       Likelihood analysis of geographic range evolution
       Likelihood analysis of geographic range evolution

       Use the command:

       module display bio/lagrange-ad55ae9

       to see exactly what this module does.



      ****************************************************

-------------------------------------------------------------------
updated: 3/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/lastz-distrib-1.02.00:

      bio/lastz-distrib-1.02.00
      ****************************************************

       This module sets up the environment for:

       MIRA 3.2.0 ( 9 Aug 2010 )
       LASTZ sequence alignment program

       Use the command:

       module display bio/lastz-distrib-1.02.00

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/libgtextutils-0.6:

      bio/libgtextutils-0.6
      ****************************************************

       This module sets up the environment for:

       Gordon-Text_utils-Library, version .6
       Description: The Gordon Text_utils (gtextutils) library is a text utilities library used by the FASTX-Toolkit, a suite of programs for biological sequence analysis.

       Use the command:

       module display bio/libgtextutils-0.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/libsequence-1.6.6:

      bio/libsequence-1.6.6
      ****************************************************

       This module sets up the environment for:

       libsequence 1.6.6
       a C++ library designed to aid writing applications for genomics and evolutionary genetics

       Use the command:

       module display bio/libsequence-1.6.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/16/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/libsequence-1.7.4:

      bio/libsequence-1.7.4
      ****************************************************

       This module sets up the environment for:

       libsequence version 1.7.4
       a C++ library designed to aid writing applications for genomics and evolutionary genetics. This module has been bult by Plamen G. Krastev.

       Use the command:

       module display bio/libsequence-1.7.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/lintre:

      bio/lintre
      ****************************************************

       This module sets up the environment for:

       lintre
       LINTRE: Software for testing the molecular clock and making linearized trees

The LINTRE programs are for (1) testing the molecular clock on a given topology of a phylogenetic tree and (2) making linearized trees (reestimating branch lengths under the assumption of constant rate of evolutions. The data that can be used are nucleotide or amino acid sequences.

For details of the methods, please look at: Phylogenetic tests of the molecular clock and linearized trees, by Naoko Takezaki, Andrey Rzhetsky, and Masatoshi Nei ( Molecular Biology and Evolution 12:823-833, 1995 ).

       Use the command:

       module display bio/lintre

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/10/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/m5tools:

      bio/m5tools
      ****************************************************

       This module sets up the environment for:

       m5tools
       M5nr database command-line tool.

       Use the command:

       module display bio/m5tools

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/09/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mach1.0.18:

      bio/mach1.0.18
      ****************************************************

       This module sets up the environment for:

       mach1.0.18
       A Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. This module was built by Plamen G. Krastev

       Use the command:

       module display bio/mach1.0.18

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mafft-6.853:

      bio/mafft-6.853
      ****************************************************

       This module sets up the environment for:

       mafft, version 6.853 (with extensions)
       Multiple alignment program for amino acid or nucleotide sequences, version 6.853

       Use the command:

       module display bio/mafft-6.853

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 5/13/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/maker-2.10:

      bio/maker-2.10
      ****************************************************

       This module sets up the environment for:

       MAKER version 2.10
       a portable and easy to configure genome annotation pipeline. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/maker-2.10

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/11/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mcl-09-308:

      bio/mcl-09-308
      ****************************************************

       This module sets up the environment for:

       MCL version 09-308
       a cluster algorithm for graphs

       Use the command:

       module display bio/mcl-09-308

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/22/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/meme-4.9.0_4:

      bio/meme-4.9.0_4
      ****************************************************

       This module sets up the environment for:

       meme v4.9.0_4
       Motif-based sequence analysis tools

       Use the command:

       module display bio/meme-4.9.0_4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079:

      bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       MEME v4.9.0_4 Parallel
       Motif-based sequence analysis tools. Compiled to run parallel jobs.

       Use the command:

       module display bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/18/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079v2:

      bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079v2
      ****************************************************

       This module sets up the environment for:

       MEME v4.9.0_4 Parallel
       Motif-based sequence analysis tools. Compiled to run parallel jobs. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/meme-4.9.0_openmpi-1.6.2_intel-13.0.079v2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/metAMOS:

      bio/metAMOS
      ****************************************************

       This module sets up the environment for:

       metAMOS 1.1
       metAMOS version 1.1
metAMOS: a modular and open source metagenomic assembly and analysis pipeline. Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. Genome Biology 14:R2 2013.
To get started on real data sets a minimum of 32 GB of RAM is recommened, and anywhere from 64-512 GB may be necessary for larger datasets.

       Use the command:

       module display bio/metAMOS

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/miRDP-1.3:

      bio/miRDP-1.3
      ****************************************************

       This module sets up the environment for:

       miRDeep-P
       miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/miRDP-1.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/miRDeep:

      bio/miRDeep
      ****************************************************

       This module sets up the environment for:

       miRDEEP
       The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data

       Use the command:

       module display bio/miRDeep

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/07/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/miRDeep2-0.0.5:

      bio/miRDeep2-0.0.5
      ****************************************************

       This module sets up the environment for:

       miRDeep2 version 0.0.5
       a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/miRDeep2-0.0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/27/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/miRcheck:

      bio/miRcheck
      ****************************************************

       This module sets up the environment for:

       miRcheck
       miRcheck contains various perl scripts useful in identfying plant miRNA genes

       Use the command:

       module display bio/miRcheck

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/23/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/migrate-3.2.6:

      bio/migrate-3.2.6
      ****************************************************

       This module sets up the environment for:

       Migrate, version 3.2.6
       Estimation of population sizes and gene flow using the coalescent

       Use the command:

       module display bio/migrate-3.2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/29/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/migrate-3.2.6_intel-12.3.174:

      bio/migrate-3.2.6_intel-12.3.174
      ****************************************************

       This module sets up the environment for:

       Migrate, version 3.2.6
       Estimation of population sizes and gene flow using the coalescent

       Use the command:

       module display bio/migrate-3.2.6_intel-12.3.174

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/migrate-3.4.4_gcc-4.7.2:

      bio/migrate-3.4.4_gcc-4.7.2
      ****************************************************

       This module sets up the environment for:

       Migrate, version 3.4.4
       Estimation of population sizes and gene flow using the coalescent

       Use the command:

       module display bio/migrate-3.4.4_gcc-4.7.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/minimac:

      bio/minimac
      ****************************************************

       This module sets up the environment for:

       minimac
       A low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. This module was built by Plamen G Krastev.

       Use the command:

       module display bio/minimac

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mira_3.2.0:

      bio/mira_3.2.0
      ****************************************************

       This module sets up the environment for:

       MIRA 3.2.0 ( 9 Aug 2010 )
       Mira Sequence Assembler

       Use the command:

       module display bio/mira_3.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/misopy-0.4.8_python-2.7.3:

      bio/misopy-0.4.8_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       misopy version 0.4.8
       a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/misopy-0.4.8_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/misopy-0.4.9_python-2.7.3:

      bio/misopy-0.4.9_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       misopy version 0.4.9
       a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/misopy-0.4.9_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/modeller-9v7:

      bio/modeller-9v7
      ****************************************************

       This module sets up the environment for:

       modeller9v7
       MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2)

       Use the command:

       module display bio/modeller-9v7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/10/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mosaik-1.0.1388:

      bio/mosaik-1.0.1388
      ****************************************************

       This module sets up the environment for:

       MOSAIK 1.0.1388
       MOSAIK is a reference-guided assembler comprising of four main modular programs

       Use the command:

       module display bio/mosaik-1.0.1388

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mothur-1.10.2:

      bio/mothur-1.10.2
      ****************************************************

       This module sets up the environment for:

       mothur, version 1.10.2
       MOTHUR seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

       Use the command:

       module display bio/mothur-1.10.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mothur-1.21.1:

      bio/mothur-1.21.1
      ****************************************************

       This module sets up the environment for:

       mothur, version 1.21.1
       MOTHUR seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

       Use the command:

       module display bio/mothur-1.21.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mothur-1.25.0:

      bio/mothur-1.25.0
      ****************************************************

       This module sets up the environment for:

       MOTHUR version 1.25.0
       MOTHUR seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. This module has been built wiht Intel compiler version 11.0.083 by Plamen G Krastev.

       Use the command:

       module display bio/mothur-1.25.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mothur-1.6.0:

      bio/mothur-1.6.0
      ****************************************************

       This module sets up the environment for:

       mothur, version 1.6
       MOTHUR seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

       Use the command:

       module display bio/mothur-1.6.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes-3.2_r268:

      bio/mrbayes-3.2_r268
      ****************************************************

       This module sets up the environment for:

       MrBayes 3.2, SVN version r268 with checkpointing, built with MPI using Intel compilers
       a free software program which performs Bayesian inference of phylogeny

       Use the command:

       module display bio/mrbayes-3.2_r268

       to see exactly what this module does.

       This build includes patches described at
       http://www.bestgrid.org/index.php/Bioinformatics_applications_at_University_of_Canterbury_HPC#Installing_MrBayes
       o fix for problem with SumP hanging in MPI on error
       o fix minor issue in mcmcdiagn param print
       o fix for 64-bit architecture
       plus a custom FAS IT RC patch
       o fix to not use readline when stdin is not a tty


      ****************************************************

-------------------------------------------------------------------
updated: 11/30/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes-3.2_r379:

      bio/mrbayes-3.2_r379
      ****************************************************

       This module sets up the environment for:

       MrBayes 3.2, SVN version r379 with checkpointing, built with MPI using Intel compilers
       a free software program which performs Bayesian inference of phylogeny

       Use the command:

       module display bio/mrbayes-3.2_r379

       to see exactly what this module does.

       This build includes patches described at
       http://www.bestgrid.org/index.php/Bioinformatics_applications_at_University_of_Canterbury_HPC#Installing_MrBayes
       o fix for problem with SumP hanging in MPI on error
       o fix minor issue in mcmcdiagn param print
       o fix for 64-bit architecture
       plus a custom FAS IT RC patch
       o fix to not use readline when stdin is not a tty


      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes-3.2_r465:

      bio/mrbayes-3.2_r465
      ****************************************************

       This module sets up the environment for:

       MrBayes, 3.2 svn revision 465
       a program for the Bayesian estimation of phylogeny, built on 2011-10-19

       Use the command:

       module display bio/mrbayes-3.2_r465

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 10/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083:

      bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       MrBayes, 3.2
       a program for the Bayesian estimation of phylogen, with beagle and customizations from Jeremy Browny

       Use the command:

       module display bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 10/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083_no_beagle:

      bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083_no_beagle
      ****************************************************

       This module sets up the environment for:

       MrBayes, 3.2
       a program for the Bayesian estimation of phylogen, without beagle, with customizations from Jeremy Browny

       Use the command:

       module display bio/mrbayes3.2_TS_openmpi-1.3.2_intel-11.0.083_no_beagle

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 10/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mrbayes3.2_TS_openmpi-1.5.3_intel-12.3.174:

      bio/mrbayes3.2_TS_openmpi-1.5.3_intel-12.3.174
      ****************************************************

       This module sets up the environment for:

       MrBayes, 3.2
       a program for the Bayesian estimation of phylogen, with beagle and customizations from Jeremy Browny

       Use the command:

       module display bio/mrbayes3.2_TS_openmpi-1.5.3_intel-12.3.174

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 10/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/msABC:

      bio/msABC
      ****************************************************

       This module sets up the environment for:

       msABC
       msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis

       Use the command:

       module display bio/msABC

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/12/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/mugsy:

      bio/mugsy
      ****************************************************

       This module sets up the environment for:

       Mugsy
       a multiple whole genome aligner. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/mugsy

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/29/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/multiz-tba.012109:

      bio/multiz-tba.012109
      ****************************************************

       This module sets up the environment for:

       multiz version tba.012109 (latest as of 2012-05-22)
       Multiz and TBA alignment programs

       Use the command:

       module display bio/multiz-tba.012109

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 5/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/muscle-3.6:

      bio/muscle-3.6
      ****************************************************

       This module sets up the environment for:

       MUSCLE version 3.6
       Multiple sequence comparison by log-expectation (MUSCLE), version 3.6

       Use the command:

       module display bio/muscle-3.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/muscle-3.8.31:

      bio/muscle-3.8.31
      ****************************************************

       This module sets up the environment for:

       MUSCLE version 3.8.31
       Multiple sequence comparison by log-expectation (MUSCLE), version 3.8.31

       Use the command:

       module display bio/muscle-3.8.31

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.22:

      bio/ncbi-blast-2.2.22
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.22
       NCBI's Basic Local Alignment Search Tool

       Use the command:

       module display bio/ncbi-blast-2.2.22

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.23+:

      bio/ncbi-blast-2.2.23+
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.23+
       NCBI's Basic Local Alignment Search Tool Plus

       Use the command:

       module display bio/ncbi-blast-2.2.23+

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.23+OLD:

      bio/ncbi-blast-2.2.23+OLD
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.23
       NCBI's Basic Local Alignment Search Tool

       Use the command:

       module display bio/ncbi-blast-2.2.23+OLD

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.25:

      bio/ncbi-blast-2.2.25
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.25
       NCBI's Basic Local Alignment Search Tool

       Use the command:

       module display bio/ncbi-blast-2.2.25

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/27/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.25+:

      bio/ncbi-blast-2.2.25+
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.25+
       NCBI's Basic Local Alignment Search Tool

       Use the command:

       module display bio/ncbi-blast-2.2.25+

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ncbi-blast-2.2.27+:

      bio/ncbi-blast-2.2.27+
      ****************************************************

       This module sets up the environment for:

       NCBI-BLAST version 2.2.27+
       NCBI's Basic Local Alignment Search Tool

       Use the command:

       module display bio/ncbi-blast-2.2.27+

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/newbler-2.5p1:

      bio/newbler-2.5p1
      ****************************************************

       This module sets up the environment for:

       newbler 2.5p1
       a software package for de novo DNA sequence assembly

       Use the command:

       module display bio/newbler-2.5p1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/19/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/nhPhyml:

      bio/nhPhyml
      ****************************************************

       This module sets up the environment for:

       nhPhyml
       a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998). This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/nhPhyml

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/novocraft-2.07.05:

      bio/novocraft-2.07.05
      ****************************************************

       This module sets up the environment for:

       novoalign version 2.07.05
       an aligner for single-ended and paired-end reads from the Illumina Genome Analyser

       Use the command:

       module display bio/novocraft-2.07.05

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/oligoarrayaux-3.8:

      bio/oligoarrayaux-3.8
      ****************************************************

       This module sets up the environment for:

       oligoarrayaux-3.8
       OligoArrayAux is a subset of the UNAFold package for use with OligoArray. This module has been built by Mike Ethier.

       Use the command:

       module display bio/oligoarrayaux-3.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/17/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/omegaMap:

      bio/omegaMap
      ****************************************************

       This module sets up the environment for:

       omegaMap
       omegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences

       Use the command:

       module display bio/omegaMap

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/orthomcl-2.0:

      bio/orthomcl-2.0
      ****************************************************

       This module sets up the environment for:

       OrthoMCL version 2.0
       Ortholog Grouping for Protein Sequences from Multiple Genomes

       Use the command:

       module display bio/orthomcl-2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/22/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pBWA-0.5.9-r30:

      bio/pBWA-0.5.9-r30
      ****************************************************

       This module sets up the environment for:

       pBWA-0.5.9-r30, compiled with intel-11.1.072 and OpenMPI 1.4.2
       pBWA is a parallel implementation of the popular software BWA.

       Use the command:

       module display bio/pBWA-0.5.9-r30

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 4/15/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pBWA-0.5.9-r32:

      bio/pBWA-0.5.9-r32
      ****************************************************

       This module sets up the environment for:

       Parallel version of Burrows-Wheeler Aligner - bwa:version 0.5.9
       Parallel version - Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

       Use the command:

       module display bio/pBWA-0.5.9-r32

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pb-mpi-1.4e_openmpi-1.6.2_intel-13.0.079:

      bio/pb-mpi-1.4e_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       PhyloBayes-MPI
       a Bayesian Markov chain Monte Carlo (MCMC) sampler for phylogenetic inference exploiting a message-passing-interface system for multi-core computing. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/pb-mpi-1.4e_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/17/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pftools-2.3.5d:

      bio/pftools-2.3.5d
      ****************************************************

       This module sets up the environment for:

       pftools vers. 2.3.5d
       pftools version 2.3.5d - protein familty tools from Philip Bucher ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/

       Use the command:

       module display bio/pftools-2.3.5d

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/27/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phase.2.1.1:

      bio/phase.2.1.1
      ****************************************************

       This module sets up the environment for:

       phase v.2.1.1
       PHASE: software for haplotype reconstruction, and recombination rate estimation from population data

       Use the command:

       module display bio/phase.2.1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/10/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phlawd:

      bio/phlawd
      ****************************************************

       This module sets up the environment for:

       phlawd
       phlawd is a PHyLogeny Assembly With Databases.

       Use the command:

       module display bio/phlawd

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phylobayes-3.2d:

      bio/phylobayes-3.2d
      ****************************************************

       This module sets up the environment for:

       PhyloBayes-3.2d
       PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.

       Use the command:

       module display bio/phylobayes-3.2d

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/13/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phylobayes-3.2f:

      bio/phylobayes-3.2f
      ****************************************************

       This module sets up the environment for:

       PhyloBayes-3.2f
       PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.

       Use the command:

       module display bio/phylobayes-3.2f

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/16/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phylobayes3.3b_intel:

      bio/phylobayes3.3b_intel
      ****************************************************

       This module sets up the environment for:

       Phylobayes3.3b
       PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.

       Use the command:

       module display bio/phylobayes3.3b_intel

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/phylocom-4.1:

      bio/phylocom-4.1
      ****************************************************

       This module sets up the environment for:

       Phylocom - v4.1
       Software for the Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic

       Use the command:

       module display bio/phylocom-4.1

       to see exactly what this module does.
      ****************************************************

-------------------------------------------------------------------
updated: 6/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pileup_v0.5:

      bio/pileup_v0.5
      ****************************************************

       This module sets up the environment for:

       SSAHA_pileup
       Pile-up pipeline for Sequence Search and Alignment by Hashing Algorithm (SSAHA2). This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/pileup_v0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pimass-lin-0.9:

      bio/pimass-lin-0.9
      ****************************************************

       This module sets up the environment for:

       pimass-lin version 0.9
       The software performs multi-SNP association with disease phenotypes. This module has been by Plamen G. Krastev.

       Use the command:

       module display bio/pimass-lin-0.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/polyscan-3.0:

      bio/polyscan-3.0
      ****************************************************

       This module sets up the environment for:

       polyscan version 3.0
       PolyScan provides de novo indel detection and SNP identification for high-throughput sequencing

       Use the command:

       module display bio/polyscan-3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/21/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/poy-4.1.2:

      bio/poy-4.1.2
      ****************************************************

       This module sets up the environment for:

       Poy v. 4.1.2 ( 5 August 2009 )
       Poy version 4.1.2 compiled with GNU and OpenMPI

       Use the command:

       module display bio/poy-4.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/24/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pplacer:

      bio/pplacer
      ****************************************************

       This module sets up the environment for:

       pplacer
       Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/pplacer

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/primer3-2.2.2-beta:

      bio/primer3-2.2.2-beta
      ****************************************************

       This module sets up the environment for:

       Primer3-2.2.2-beta
       Widely used program for designing PCR primers - Polymerase Chain Reaction

       Use the command:

       module display bio/primer3-2.2.2-beta

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/27/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/probabel-0.3.0:

      bio/probabel-0.3.0
      ****************************************************

       This module sets up the environment for:

       probabel version 0.3.0
       a genome-wide association analysis tool for imputed data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/probabel-0.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/prodigal.v2_60:

      bio/prodigal.v2_60
      ****************************************************

       This module sets up the environment for:

       Prodigal version 2_60
       Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Module built my Mike Ethier.

       Use the command:

       module display bio/prodigal.v2_60

       to see exactly what this module does.
      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/promals_package:

      promals_package module
      ****************************************************

       This module sets up the following environment
       variables for promals_package:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 7/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/prot4EST-3.1b:

      bio/prot4EST-3.1b
      ****************************************************

       This module sets up the environment for:

       prot4EST
       EST protein translation suite

       Use the command:

       module display bio/prot4EST-3.1b

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 5/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/psortb-3.0.3:

      bio/psortb-3.0.3
      ****************************************************

       This module sets up the environment for:

       psortb vers. 3.0.3
       psortb version 3.0.3 - Finds protein sub-cellular localization http://www.psort.org/downloads/index.html. Config files are in /n/sw/psortb-3.0.3/psort/conf

       Use the command:

       module display bio/psortb-3.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/27/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pybedtools-0.6.1:

      bio/pybedtools-0.6.1
      ****************************************************

       This module sets up the environment for:

       pybedtools version 0.6.1
       a Python wrapper for Aaron Quinlan's BEDtools and extends genome-algebra programs by offering feature-level manipulations from with Python. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/pybedtools-0.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pycogent-1.5:

      bio/pycogent-1.5
      ****************************************************

       This module sets up the environment for:

       PyCogent, version 1.5
       Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

       Use the command:

       module display bio/pycogent-1.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pycogent-1.5.1:

      bio/pycogent-1.5.1
      ****************************************************

       This module sets up the environment for:

       PyCogent, version 1.5.1
       Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution

       Use the command:

       module display bio/pycogent-1.5.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pycogent-1.5.3_python-2.7.3:

      bio/pycogent-1.5.3_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       PyCogent version 1.5.3
       a software library for genomic biology. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/pycogent-1.5.3_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pyfasta-0.4.5_python-2.7.3:

      bio/pyfasta-0.4.5_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       PyFasta version 0.4.5
       a fast, memory-efficient, pythonic (and command-line) access to fasta sequence files. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/pyfasta-0.4.5_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pygr-0.8.2_python-2.7.1:

      bio/pygr-0.8.2_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       Pygr version 0.8.2
       Pygr is open source software designed to make it easy to do powerful sequence and comparative genomics analyses. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/pygr-0.8.2_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/27/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pynast-1.2_python-2.7.3:

      bio/pynast-1.2_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       PyNAST version 1.2
       a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rDNA sequences to existing 16s rDNA alignments. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/pynast-1.2_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pynast-2012-01-05:

      bio/pynast-2012-01-05
      ****************************************************

       This module sets up the environment for:

       PyNAST, built from svn source 2012-01-05
       Python Nearest Alignment Space Termination Tool

       Use the command:

       module display bio/pynast-2012-01-05

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 1/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pyronoise-2:

      bio/pyronoise-2
      ****************************************************

       This module sets up the environment for:

       PyroNoise2
       The diversity estimation software used in Quince et al. 'Noise and the Accurate Determination of Microbial Diversity from 454 Pyrosequencing Data'.

       Use the command:

       module display bio/pyronoise-2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/27/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pysam:

      bio/pysam
      ****************************************************

       This module sets up the environment for:

       SAM Tools version 0.1.12a
       utilities for manipulating alignments in the Sequence Alignment/Map format

       Use the command:

       module display bio/pysam

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pysam-0.7.4_python-2.7.3:

      bio/pysam-0.7.4_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       PySam version 0.7.4
       a python module for reading and manipulating Samfiles. This module was built with Python version 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/pysam-0.7.4_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Plamen G. Krastev

      ****************************************************

-------------------------------------------------------------------
updated: 2/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/pyvcf_python-2.7.3:

      bio/pyvcf_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       PyVCF
       a Variant Call Format (VCF) reader for Python. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/pyvcf_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.1.0:

      bio/qiime-1.1.0
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.1.0
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-1.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.2.1:

      bio/qiime-1.2.1
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.2.1
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-1.2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/22/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.2.1-release:

      bio/qiime-1.2.1-release
      ****************************************************

       This module sets up the environment for:

       qiime version 1.2.1 (from release script)
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-1.2.1-release

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/10/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.3.0:

      bio/qiime-1.3.0
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.3.0
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-1.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/03/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.4.0:

      bio/qiime-1.4.0
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.4.0
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-1.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.5.0:

      bio/qiime-1.5.0
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.5.0
       QIIME: Quantitative Insights Into Microbial Ecology. This module was built by Plamen G. Krastev.

       Use the command:

       module display bio/qiime-1.5.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-1.6.0:

      bio/qiime-1.6.0
      ****************************************************

       This module sets up the environment for:

       qiime, version 1.6.0
       QIIME: Quantitative Insights Into Microbial Ecology. This module was built by Plamen G. Krastev.

       Use the command:

       module display bio/qiime-1.6.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/qiime-r1719:

      bio/qiime-r1719
      ****************************************************

       This module sets up the environment for:

       qiime, development version r1719
       QIIME: Quantitative Insights Into Microbial Ecology

       Use the command:

       module display bio/qiime-r1719

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/quake-0.3.1:

      bio/quake-0.3.1
      ****************************************************

       This module sets up the environment for:

       Quake version 0.3.1
       A package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/quake-0.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/11/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/randfold-2.0:

      bio/randfold-2.0
      ****************************************************

       This module sets up the environment for:

       randfold version 2.0
       The software computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/randfold-2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/27/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ray-0.0.7:

      bio/ray-0.0.7
      ****************************************************

       This module sets up the environment for:

       Ray 0.0.7 ( 9 Aug 2010 )
       parallel genome assembler

       Use the command:

       module display bio/ray-0.0.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rcngs_v1:

      bio/rcngs_v1
      ****************************************************

       This module sets up the environment for:

       rcngs Version 1
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/rcngs_v1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/08/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rcngs_v2:

      bio/rcngs_v2
      ****************************************************

       This module sets up the environment for:

       rcngs Version 1
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/rcngs_v2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/24/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rcngs_v3:

      bio/rcngs_v3
      ****************************************************

       This module sets up the environment for:

       rcngs Version 1
       Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers

       Use the command:

       module display bio/rcngs_v3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/recon-1.06:

      bio/recon-1.06
      ****************************************************

       This module sets up the environment for:

       RECON version 1.6 (patched by RepeatMasker.org)
       a package for automated de novo identification of repeat families from genomic sequences

       Use the command:

       module display bio/recon-1.06

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/recon-1.07:

      bio/recon-1.07
      ****************************************************

       This module sets up the environment for:

       RECON version 1.6 (patched by RepeatMasker.org)
       a package for automated de novo identification of repeat families from genomic sequences

       Use the command:

       module display bio/recon-1.07

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/relion-1.0:

      bio/relion-1.0
      ****************************************************

       This module sets up the environment for:

       RELION version 1.0
       a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/relion-1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/relion-1.1:

      bio/relion-1.1
      ****************************************************

       This module sets up the environment for:

       RELION version 1.1
       a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/relion-1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/relion-1.1_v2:

      bio/relion-1.1_v2
      ****************************************************

       This module sets up the environment for:

       RELION version 1.1
       a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/relion-1.1_v2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/11/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/relion-1.2:

      bio/relion-1.2
      ****************************************************

       This module sets up the environment for:

       RELION version 1.2
       a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/relion-1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/10/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/repeatmasker-3.2.8:

      bio/repeatmasker-3.2.8
      ****************************************************

       This module sets up the environment for:

       RepeatMasker version 3.2.8
       a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences

       Use the command:

       module display bio/repeatmasker-3.2.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/repeatmodeler-1.0.3:

      bio/repeatmodeler-1.0.3
      ****************************************************

       This module sets up the environment for:

       RepeatModeler version 1.0.3
       a de-novo repeat family identification and modeling package

       Use the command:

       module display bio/repeatmodeler-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/repeatmodeler-1.0.5:

      bio/repeatmodeler-1.0.5
      ****************************************************

       This module sets up the environment for:

       RepeatModeler version 1.0.5
       a de-novo repeat family identification and modeling package

       Use the command:

       module display bio/repeatmodeler-1.0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/30/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/repeatscout-1.0.5:

      bio/repeatscout-1.0.5
      ****************************************************

       This module sets up the environment for:

       RepeatScout version 1.0.5
       a tool to discover repetitive substrings in DNA

       Use the command:

       module display bio/repeatscout-1.0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ribopicker-standalone-0.4.3:

      bio/ribopicker-standalone-0.4.3
      ****************************************************

       This module sets up the environment for:

       riboPicker version 0.4.3
       identifies and removes rRNA sequences that are similar to known rRNA sequences.

       Use the command:

       module display bio/ribopicker-standalone-0.4.3

       to see exactly what this module does.

       This module was built by:

       rchelp@fas.harvard.edu

      ****************************************************

-------------------------------------------------------------------
updated: 4/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rnaplex-1.0.0:

      bio/rnaplex-1.0.0
      ****************************************************

       This module sets up the environment for:

       RNAplex
       a fast tool for RNA-RNA interaction search

       Use the command:

       module display bio/rnaplex-1.0.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/01/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rosetta3.1:

      bio/rosetta3.1
      ****************************************************

       This module sets up the environment for:

       rosetta version 3.1
       System for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions

       Use the command:

       module display bio/rosetta3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rseg:

      bio/rseg
      ****************************************************

       This module sets up the environment for:

       TopHat version 1.0.12 (Beta)
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/rseg

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rsem-1.1.13:

      bio/rsem-1.1.13
      ****************************************************

       This module sets up the environment for:

       rsem version 1.1.13
       RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The new RSEM package (rsem-1.x) provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. It can also generate genomic-coordinate BAM files and UCSC wiggle files for visualization. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels.

       Use the command:

       module display bio/rsem-1.1.13

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rtax-0.981:

      bio/rtax-0.981
      ****************************************************

       This module sets up the environment for:

       RTAX version 0.981
       Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/rtax-0.981

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rtax-0.983:

      bio/rtax-0.983
      ****************************************************

       This module sets up the environment for:

       RTAX version 0.983
       Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/rtax-0.983

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/rum:

      bio/rum
      ****************************************************

       This module sets up the environment for:

       rum
       RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

       Use the command:

       module display bio/rum

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/samtools-0.1.12a:

      bio/samtools-0.1.12a
      ****************************************************

       This module sets up the environment for:

       SAM Tools version 0.1.12a
       utilities for manipulating alignments in the Sequence Alignment/Map format

       Use the command:

       module display bio/samtools-0.1.12a

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/13/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/samtools-0.1.18:

      bio/samtools-0.1.18
      ****************************************************

       This module sets up the environment for:

       SAM Tools version 0.1.18
       utilities for manipulating alignments in the Sequence Alignment/Map format

       Use the command:

       module display bio/samtools-0.1.18

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/samtools-0.1.18_zlib-1.2.5:

      bio/samtools-0.1.18_zlib-1.2.5
      ****************************************************

       This module sets up the environment for:

       SAMTOOLS
       SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.. This module has been built with zlib version 1.2.5 by Plamen G. Krastev.

       Use the command:

       module display bio/samtools-0.1.18_zlib-1.2.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/samtools-0.1.7:

      samtools module
      ****************************************************

       This module sets up the following environment
       variables for samtools version 0.1.7:
       PATH
       MANPATH

      ****************************************************

-------------------------------------------------------------------
updated: 6/30/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sap-1.0.12:

      bio/sap-1.0.12
      ****************************************************

       This module sets up the environment for:

       SAP version 1.0.12
       Statistical Assignmnet Package, Version 1.0.12

       Use the command:

       module display bio/sap-1.0.12

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/06/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/scan_for_matches:

      bio/scan_for_matches
      ****************************************************

       This module sets up the environment for:

       scan_for_matches
       A Program to Scan Nucleotide or Protein Sequences for Matching Patterns

       Use the command:

       module display bio/scan_for_matches

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/scan_for_matches-5.8.2013:

      bio/scan_for_matches-5.8.2013
      ****************************************************

       This module sets up the environment for:

       scan_for_matches
       A Program to Scan Nucleotide or Protein Sequences for Matching Patterns

       Use the command:

       module display bio/scan_for_matches-5.8.2013

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/segway-1.1.0_python-2.7.1:

      bio/segway-1.1.0_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       segway version 1.1.0
       a novel method for analyzing multiple tracks of functional genomics data. This module was built by Plamen G Krastev.

       Use the command:

       module display bio/segway-1.1.0_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sff2fastq:

      bio/sff2fastq
      ****************************************************

       This module sets up the environment for:

       sff2fastq -- version: 0.8.0
       sff2fastq extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format

       Use the command:

       module display bio/sff2fastq

       to see exactly what this module does.
      ****************************************************

-------------------------------------------------------------------
updated: 5/10/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sfscode-20100203:

      bio/sfscode-20100203
      ****************************************************

       This module sets up the environment for:

       SFS_code version 20100203
       Selection on Finite Sites under COmplex Demographic Events

       Use the command:

       module display bio/sfscode-20100203

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/06/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sga-0.9.34:

      bio/sga-0.9.34
      ****************************************************

       This module sets up the environment for:

       SGA string graph assembler version 0.9.34
       SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

       Use the command:

       module display bio/sga-0.9.34

       to see exactly what this module does.
run by :sga
      ****************************************************

-------------------------------------------------------------------
updated: 8/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/shore-0.4.1beta:

      bio/shore-0.4.1beta
      ****************************************************

       This module sets up the environment for:

       Shore v. 0.4.1Beta ( 06 Sep 2009 )
       Shore is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer

       Use the command:

       module display bio/shore-0.4.1beta

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/30/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/shore-0.5.0beta:

      bio/shore-0.5.0beta
      ****************************************************

       This module sets up the environment for:

       Shore v. 0.5.0Beta ( 07 July 2010 )
       Shore is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer

       Use the command:

       module display bio/shore-0.5.0beta

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sickle-master-1.200:

      bio/sickle-master-1.200
      ****************************************************

       This module sets up the environment for:

       Sickle-master version 1.200
       sickle - A windowed adaptive trimming tool for FASTQ files using quality. This module has been built by Mike Ethier.

       Use the command:

       module display bio/sickle-master-1.200

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/21/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/smalt-0.6.1:

      bio/smalt-0.6.1
      ****************************************************

       This module sets up the environment for:

       SMALT version 0.6.1
       SMALT efficiently aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired-end reads. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/smalt-0.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/smrtanalysis-1.3.3:

      bio/smrtanalysis-1.3.3
      ****************************************************

       This module sets up the environment for:

       smrtanalysis version 1.3.3
       SMRT Analysis is PacBio's bioinformatics software suite for processing single molecule real time DNA sequencing data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/smrtanalysis-1.3.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/24/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/smrtanalysis-1.4.0:

      bio/smrtanalysis-1.4.0
      ****************************************************

       This module sets up the environment for:

       smrtanalysis version 1.4
       SMRT Analysis is PacBio's bioinformatics software suite for processing single molecule real time DNA sequencing data. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/smrtanalysis-1.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/snpEff-3.2a:

      bio/snpEff-3.2a
      ****************************************************

       This module sets up the environment for:

       snpEff version 3.2a
       Genetic variant annotation and effect prediction toolbox.. This module has been built by Mike Ethier.

       Use the command:

       module display bio/snpEff-3.2a

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/snpomatic:

      bio/snpomatic
      ****************************************************

       This module sets up the environment for:

       SNP-O-Matic
       a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/snpomatic

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/soap-2.20:

      bio/soap-2.20
      ****************************************************

       This module sets up the environment for:

       SOAP, version 2.20
       Updated version of SOAP software for short oligonucleotide alignment

       Use the command:

       module display bio/soap-2.20

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/soapdenovo-1.04:

      bio/soapdenovo-1.04
      ****************************************************

       This module sets up the environment for:

       SOAPdenovo, version 1.04
       SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.

       Use the command:

       module display bio/soapdenovo-1.04

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/16/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/soapdenovo-1.05:

      bio/soapdenovo-1.05
      ****************************************************

       This module sets up the environment for:

       SOAPdenovo, version 1.05
       SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.

       Use the command:

       module display bio/soapdenovo-1.05

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/05/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/soapdenovo-2.04:

      bio/soapdenovo-2.04
      ****************************************************

       This module sets up the environment for:

       SOAPdenovo version 2.04
       a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/soapdenovo-2.04

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sqlite-3.7.5:

      bio/sqlite-3.7.5
      ****************************************************

       This module sets up the environment for:

       sqlite, version 3.7.5
       SQL database engine.

       Use the command:

       module display bio/sqlite-3.7.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sqlitewrapped-1.3.1:

      bio/sqlitewrapped-1.3.1
      ****************************************************

       This module sets up the environment for:

       sqlitewrapped, version 1.3.1
       C++ wrapper for the Sqlite database C application programming interface

       Use the command:

       module display bio/sqlitewrapped-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/squid-1.9g:

      bio/squid-1.9g
      ****************************************************

       This module sets up the environment for:

       SQUID version 1.9g
       a freely redistributable library of C code functions for sequence analysis. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/squid-1.9g

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/27/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sra_sdk-2.0.0b6:

      bio/sra_sdk-2.0.0b6
      ****************************************************

       This module sets up the environment for:

       SRA Toolkit, version 2.0.0b6
       NCBI SRA Software Development Kit, version 2.0.0b6

       Use the command:

       module display bio/sra_sdk-2.0.0b6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/sratoolkit.2.1.10:

      bio/sratoolkit.2.1.10
      ****************************************************

       This module sets up the environment for:

       SRA Toolkit, version 2.1.10
       NCBI SRA Software Development Kit, version 2.1.10

       Use the command:

       module display bio/sratoolkit.2.1.10

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/ssaha2-2.5.4:

      bio/ssaha2-2.5.4
      ****************************************************

       This module sets up the environment for:

       ssaha2, version 2.5.4
       SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

       Use the command:

       module display bio/ssaha2-2.5.4

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 9/24/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stacks-0.99994:

      bio/stacks-0.99994
      ****************************************************

       This module sets up the environment for:

       stacks version 0.99994
       a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/stacks-0.99994

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/27/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/staden-2.0.0b9:

      bio/staden-2.0.0b9
      ****************************************************

       This module sets up the environment for:

       staden, version 2.0.0b9
       A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools.

       Use the command:

       module display bio/staden-2.0.0b9

       to see exactly what this module does.

       This module was built by:

       jzhang

      ****************************************************

-------------------------------------------------------------------
updated: 4/24/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stamatak-standard-RAxML-03-07-2011:

      bio/stamatak-standard-RAxML-03-07-2011
      ****************************************************

       This module sets up the environment for:

       RAxML latest from github - v7.3.0, MPI enabled - downloaded on 3/7/2012
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/stamatak-standard-RAxML-03-07-2011

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stamatak-standard-RAxML-11-02-2011:

      bio/stamatak-standard-RAxML-11-02-2011
      ****************************************************

       This module sets up the environment for:

       RAxML latest from github - v7.3.0, MPI enabled
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees.

       Use the command:

       module display bio/stamatak-standard-RAxML-11-02-2011

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stamatak-standard-RAxML-4-29-2013:

      bio/stamatak-standard-RAxML-4-29-2013
      ****************************************************

       This module sets up the environment for:

       RAxML latest from github - v7.4.9, MPI enabled
       RAxML (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. Module built by Mike Ethier

       Use the command:

       module display bio/stamatak-standard-RAxML-4-29-2013

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stampy-1.0.10:

      bio/stampy-1.0.10
      ****************************************************

       This module sets up the environment for:

       stampy version 1.0.10
       a package for the mapping of short reads from illumina sequencing machines onto a reference genome

       Use the command:

       module display bio/stampy-1.0.10

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stampy-1.0.18:

      bio/stampy-1.0.18
      ****************************************************

       This module sets up the environment for:

       stampy version 1.0.18
       a package for the mapping of short reads from illumina sequencing machines onto a reference genome

       Use the command:

       module display bio/stampy-1.0.18

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stampy-1.0.18_python2.7.3:

      bio/stampy-1.0.18_python2.7.3
      ****************************************************

       This module sets up the environment for:

       stampy version 1.0.18
       a package for the mapping of short reads from illumina sequencing machines onto a reference genome

       Use the command:

       module display bio/stampy-1.0.18_python2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/27/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/stampy-1.0.21_python2.7.3:

      bio/stampy-1.0.21_python2.7.3
      ****************************************************

       This module sets up the environment for:

       stampy version 1.0.21
       a package for the mapping of short reads from illumina sequencing machines onto a reference genome

       Use the command:

       module display bio/stampy-1.0.21_python2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/27/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/structure2.3.1:

      bio/structure2.3.1
      ****************************************************

       This module sets up the environment for:

       Structure Version 2.3.1
       The program structure is a free software package for using multi-locus genotype data to investigate population structure. http://pritch.bsd.uchicago.edu/structure.html

       Use the command:

       module display bio/structure2.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/06/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/swipe-2.0.5:

      bio/swipe-2.0.5
      ****************************************************

       This module sets up the environment for:

       swipe version 2.0.5
       a tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/swipe-2.0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/symap:

      bio/symap
      ****************************************************

       This module sets up the environment for:

       symap,version 3.5
       SyMAP (Synteny Mapping and Analysis Program) is a software package for detecting and displaying syntenic relationships between sequences.

       Use the command:

       module display bio/symap

       to see exactly what this module does.
run as: symap

      ****************************************************

-------------------------------------------------------------------
updated: 5/04/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/t_coffee-8.69:

      bio/t_coffee-8.69
      ****************************************************

       This module sets up the environment for:

       T-COFFEE 8.69
       n/a

       Use the command:

       module display bio/t_coffee-8.69

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/23/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tabix-0.2.6:

      bio/tabix-0.2.6
      ****************************************************

       This module sets up the environment for:

       tabix version 0.2.6
       indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/tabix-0.2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tandem-10-01-01-4:

      bio/tandem-10-01-01-4
      ****************************************************

       This module sets up the environment for:

       X! Tandem 10-01-01-4
       X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification

       Use the command:

       module display bio/tandem-10-01-01-4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tax2tree-1.0_python-2.7.3:

      bio/tax2tree-1.0_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       tax2tree version 1.0
       Tools for decorating taxonomy information on to a phylogenetic tree. This module has been built with Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display bio/tax2tree-1.0_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tess-2.3.1:

      bio/tess-2.3.1
      ****************************************************

       This module sets up the environment for:

       TESS, version 2.3.1
       Bayesian Clustering using tessellations and Markov models for spatial population genetics.

       Use the command:

       module display bio/tess-2.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/15/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tnt:

      bio/tnt
      ****************************************************

       This module sets up the environment for:

       TNT
       a program for phylogenetic analysis under parsimony (with very fast tree-searching algorithms; Nixon, 1999, Cladistics 15:407-406; Goloboff, 1999, Cladistics 15:407-428), as well as extensive tree handling and diagnosis capabilities. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/tnt

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/04/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-1.0.12:

      bio/tophat-1.0.12
      ****************************************************

       This module sets up the environment for:

       TopHat version 1.0.12 (Beta)
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/tophat-1.0.12

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/10/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-1.1.4:

      bio/tophat-1.1.4
      ****************************************************

       This module sets up the environment for:

       TopHat version 1.0.12 (Beta)
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/tophat-1.1.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/18/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-1.3.2:

      bio/tophat-1.3.2
      ****************************************************

       This module sets up the environment for:

       TopHat version 1.3.2 (Beta)
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/tophat-1.3.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-1.4.0:

      bio/tophat-1.4.0
      ****************************************************

       This module sets up the environment for:

       TopHat version 1.4.0
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/tophat-1.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-2.0.4.Linux_x86_64:

      bio/tophat-2.0.4.Linux_x86_64
      ****************************************************

       This module sets up the environment for:

       TopHat version 2.0.4
       TopHat is a fast splice junction mapper for RNA-Seq reads.

       Use the command:

       module display bio/tophat-2.0.4.Linux_x86_64

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/07/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/tophat-2.0.7.Linux_x86_64:

      bio/tophat-2.0.7.Linux_x86_64
      ****************************************************

       This module sets up the environment for:

       TopHat version 2.0.7
       TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

       Use the command:

       module display bio/tophat-2.0.7.Linux_x86_64

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/23/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trans-ABySS:

      bio/trans-ABySS
      ****************************************************

       This module sets up the environment for:

       Trans-ABySS Analysis Pipeline v1.2.0
       Trans-ABySS analysis pipeline is a suite of programs that are used to process transcriptome assemblies and find novel events and perform various other transcriptome analyses

       Use the command:

       module display bio/trans-ABySS

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trans-ABySS-v1.3.2:

      bio/trans-ABySS-v1.3.2
      ****************************************************

       This module sets up the environment for:

       trans-ABySS v1.3.2
       Trans-ABySS is an analysis pipeline for post-processing ABySS assemblies of transcriptome sequencing data. It addresses varying transcript expression levels by processing multiple assemblies across a range of k values (Robertson et al. 2010).

       Use the command:

       module display bio/trans-ABySS-v1.3.2

       to see exactly what this module does.
must run source /n/sw/trans-ABySS-v1.3.2/setup
      ****************************************************

-------------------------------------------------------------------
updated: 6/16/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/treePL:

      bio/treePL
      ****************************************************

       This module sets up the environment for:

       treePL
       Phylogenetic penalized likelihood

       Use the command:

       module display bio/treePL

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/19/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/treePL-master-3.26.2013:

      bio/treePL-master-3.26.2013
      ****************************************************

       This module sets up the environment for:

       treePL
       Phylogenetic penalized likelihood

       Use the command:

       module display bio/treePL-master-3.26.2013

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trimgalore-0.2.5:

      bio/trimgalore-0.2.5
      ****************************************************

       This module sets up the environment for:

       Trim Galore version 0.2.5
       a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/trimgalore-0.2.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/31/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trimgalore-0.2.6:

      bio/trimgalore-0.2.6
      ****************************************************

       This module sets up the environment for:

       Trim Galore version 0.2.6
       a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/trimgalore-0.2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq:

      bio/trinityrnaseq
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2011-07-13 Pipeline,version 2011-07-13
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

       Use the command:

       module display bio/trinityrnaseq

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --left reads_1.fq --right reads_2.fq --CPU 4 --run_butterfly --bflyHeapSpace 10G
JVM argument -Xmx10g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 8/04/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq_2011_08_20:

      bio/trinityrnaseq_2011_08_20
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2011-08-20 Pipeline,version 2011-08-20
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

       Use the command:

       module display bio/trinityrnaseq_2011_08_20

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --left reads_1.fq --right reads_2.fq --CPU 4 --run_butterfly --bflyHeapSpace 10G
JVM argument -Xmx10g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq_r2012-01-25:

      bio/trinityrnaseq_r2012-01-25
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2012-01-25 Pipeline,version 2012-01-25
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

       Use the command:

       module display bio/trinityrnaseq_r2012-01-25

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --left reads_1.fq --right reads_2.fq --CPU 4 --run_butterfly --bflyHeapSpace 10G
JVM argument -Xmx10g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq_r2012-05-18:

      bio/trinityrnaseq_r2012-05-18
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2012-05-18 Pipeline,version 2012-05-18
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

       Use the command:

       module display bio/trinityrnaseq_r2012-05-18

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --left reads_1.fq --right reads_2.fq --CPU 4 --run_butterfly --bflyHeapSpace 10G
JVM argument -Xmx10g is recommended
      ****************************************************

-------------------------------------------------------------------
updated: 6/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq_r2012-06-08:

      bio/trinityrnaseq_r2012-06-08
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2012-06-08 Pipeline,version 2012-06-08
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

       Use the command:

       module display bio/trinityrnaseq_r2012-06-08

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --JM 100G --left reads_1.fq --right reads_2.fq --CPU 6
      ****************************************************

-------------------------------------------------------------------
updated: 6/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/trinityrnaseq_r2012-10-05:

      bio/trinityrnaseq_r2012-10-05
      ****************************************************

       This module sets up the environment for:

       trinityrnaseq_r2012-10-05 Pipeline,version 2012-10-05
       Trinity, developed at the Broad Institute, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/trinityrnaseq_r2012-10-05

       to see exactly what this module does. http://trinityrnaseq.sourceforge.net/#sample_data
Trinity.pl --seqType fq --JM 100G --left reads_1.fq --right reads_2.fq --CPU 6
      ****************************************************

-------------------------------------------------------------------
updated: 10/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/uclust-1.2.21q:

      bio/uclust-1.2.21q
      ****************************************************

       This module sets up the environment for:

       UCLUST version 1.2.21q
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity.

       Use the command:

       module display bio/uclust-1.2.21q

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/uclust-1.2.22:

      bio/uclust-1.2.22
      ****************************************************

       This module sets up the environment for:

       UCLUST version 1.2.22
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity.

       Use the command:

       module display bio/uclust-1.2.22

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/umake-1.0.1.20110706:

      bio/umake-1.0.1.20110706
      ****************************************************

       This module sets up the environment for:

       UMAKE version 1.0.1.20110706
       a software pipeline to detect SNPs and call their genotypes from a list of BAM files. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/umake-1.0.1.20110706

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/21/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/unafold-3.8:

      bio/unafold-3.8
      ****************************************************

       This module sets up the environment for:

       unafold 3.8
       Unified Nucleic Acid Folding and hybridization package

       Use the command:

       module display bio/unafold-3.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/06/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/usearch4.1.93:

      bio/usearch4.1.93
      ****************************************************

       This module sets up the environment for:

       USEARCH version 4.1.93
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity.

       Use the command:

       module display bio/usearch4.1.93

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/usearch5.0.151:

      bio/usearch5.0.151
      ****************************************************

       This module sets up the environment for:

       USEARCH version 5.0.151
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity.

       Use the command:

       module display bio/usearch5.0.151

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/usearch5.1.221:

      bio/usearch5.1.221
      ****************************************************

       This module sets up the environment for:

       USEARCH version 5.1.221
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/usearch5.1.221

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/usearch5.2.236:

      bio/usearch5.2.236
      ****************************************************

       This module sets up the environment for:

       USEARCH version 5.2.236
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/usearch5.2.236

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/15/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/usearch5.2.32:

      bio/usearch5.2.32
      ****************************************************

       This module sets up the environment for:

       USEARCH version 5.2.32
       USEARCH is an algorithm designed to enable high-throughput, sensitive search of very large sequence databases. USEARCH is orders of magnitude faster than BLAST for some applications. UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity. This module has been built by Plamen G Krastev.

       Use the command:

       module display bio/usearch5.2.32

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/vcftools_0.1.9:

      bio/vcftools_0.1.9
      ****************************************************

       This module sets up the environment for:

       vcftools version 0.1.9
       a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. This module has been built by Plamen G. Krastev.

       Use the command:

       module display bio/vcftools_0.1.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/velvet-sc:

      bio/velvet-sc
      ****************************************************

       This module sets up the environment for:

       velvet-sc
       Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

       Use the command:

       module display bio/velvet-sc

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/04/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/vmatch-2.1.7:

      bio/vmatch-2.1.7
      ****************************************************

       This module sets up the environment for:

       vmatch - 2.1.7
       vmatch is a tool for efficiently solving large scale sequence matching tasks. This module has been built by Mike Ethier.

       Use the command:

       module display bio/vmatch-2.1.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/weblogo:

      bio/weblogo
      ****************************************************

       This module sets up the environment for:

       weblogo
       draw seqlogo

       Use the command:

       module display bio/weblogo

      ****************************************************

-------------------------------------------------------------------
updated: 7/29/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/wise2.2.0:

      bio/wise2.2.0
      ****************************************************

       This module sets up the environment for:

       wise2 version 2.2.0
       Wise2 is a package focused on comparisons of bio polymers, commonly DNA sequence and protein sequence.Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. There is currently no other package that I know of that contains this type of algorithm with a full blown gene prediction model and a hidden Markov model of a protein domain.

       Use the command:

       module display bio/wise2.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/bio/xmfa2struct:

      bio/xmfa2struct
      ****************************************************

       This module sets up the environment for:

       xmfa2struct
       xmfa2struct is a program written in C which converts files in eXtended Multi-Fasta format (XMFA, the input format of ClonalFrame) into the input file format of Structure.

       Use the command:

       module display bio/xmfa2struct

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/OpenCV-2.3.1a:

      centos6/OpenCV-2.3.1a
      ****************************************************

       This module sets up the environment for:

       OpenCV, version OpenCV-2.3.1a, including python module cv (for python 2.7)
       Open Source Computer Vision -- is a library of programming functions for real time computer vision

       Use the command:

       module display centos6/OpenCV-2.3.1a

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/SuiteSparse-4.0.2:

      centos6/SuiteSparse-4.0.2
      ****************************************************

       This module sets up the environment for:

       SuiteSparse version 4.0.2
       Tim Davis's sparse matrix packages

       Use the command:

       module display centos6/SuiteSparse-4.0.2

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/atlas-3.10.1:

      centos6/atlas-3.10.1
      ****************************************************

       This module sets up the environment for:

       ATLAS version 3.10.1
       Automatically Tuned Linear Algebra Software

       Use the command:

       module display centos6/atlas-3.10.1

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/fftw-2.1.5_openmpi-1.6.3_intel-13.0.079:

      centos6/fftw-2.1.5_openmpi-1.6.3_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 13.0.079 and OpenMPI 1.6.3 with thread support
       FFTW 2.1.5, compiled with Intel 13.0.079 and OpenMPI 1.6.3 with thread support

       Use the command:

       module display centos6/fftw-2.1.5_openmpi-1.6.3_intel-13.0.079

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 3/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/fftw-3.3.3:

      centos6/fftw-3.3.3
      ****************************************************

       This module sets up the environment for:

       FFTW version 3.3.3
       a C subroutine library for computing the discrete Fourier transform

       Use the command:

       module display centos6/fftw-3.3.3

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/gcc-4.8.0:

      centos6/gcc-4.8.0
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.8.0
       GNU compiler version 4.8.0. This module has been built by Paul Edmon.

       Use the command:

       module display centos6/gcc-4.8.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/geos-3.3.8:

      centos6/geos-3.3.8
      ****************************************************

       This module sets up the environment for:

       GEOS version 3.3.8
       GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). Build by Paul Edmon

       Use the command:

       module display centos6/geos-3.3.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/gmp-5.1.1:

      centos6/gmp-5.1.1
      ****************************************************

       This module sets up the environment for:

       GMP version 5.1.1
       a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. This module has been built with GCC 4.4.6 by Paul Edmon.

       Use the command:

       module display centos6/gmp-5.1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/gsl-1.15_intel-13.0.079:

      centos6/gsl-1.15_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       GNU Science Library 1.15
       GNU Science Library 1.15 compiled with Intel 13.0.079 compilers

       Use the command:

       module display centos6/gsl-1.15_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/gtk+-2.24.4:

      centos6/gtk+-2.24.4
      ****************************************************

       This module sets up the environment for:

       GTK+ version 2.24.4, including glib, pixman, cairo, pango, atk, and many more
       a library to build graphical user interfaces (GUIs) originally for X Windows

       Use the command:

       module display centos6/gtk+-2.24.4

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/hdf5-1.8.10-patch1_openmpi-1.6.3_intel-13.0.079:

      centos6/hdf5-1.8.10-patch1_openmpi-1.6.3_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       hdf5 v1.8.10 patch 1 with OpenMPI 1.6.3 and Intel 13.0.079 Compilers
       HDF5 version 1.8.10 patch 1 compiled with OpenMPI 1.6.3 and Intel 13.0.079 compilers with fortran and parallel bindings.

       Use the command:

       module display centos6/hdf5-1.8.10-patch1_openmpi-1.6.3_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/ipython-0.10.2_python-2.7:

      centos6/ipython-0.10.2_python-2.7
      ****************************************************

       This module sets up the environment for:

       IPython version 0.10.2, built for python 2.7
       an enhanced interactive Python shell and architecture for interactive parallel computing

       Use the command:

       module display centos6/ipython-0.10.2_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/matplotlib-1.0.0_python-2.7:

      centos6/matplotlib-1.0.0_python-2.7
      ****************************************************

       This module sets up the environment for:

       matplotlib version 1.0.0, built for python 2.7
       a python 2D plotting library

       Use the command:

       module display centos6/matplotlib-1.0.0_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/mpc-1.0.1:

      centos6/mpc-1.0.1
      ****************************************************

       This module sets up the environment for:

       MPC version 1.0.1
       a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. This module has been built with GCC 4.4.6 by Paul Edmon.

       Use the command:

       module display centos6/mpc-1.0.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/mpfr-3.1.2:

      centos6/mpfr-3.1.2
      ****************************************************

       This module sets up the environment for:

       MPFR version 3.1.2
       a C library for multiple-precision floating-point computations with correct rounding. This module has been built with GCC 4.4.6 by Paul Edmon.

       Use the command:

       module display centos6/mpfr-3.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/13/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/netcdf-3.6.3_intel-13.0.079:

      centos6/netcdf-3.6.3_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       network Common Data Form, version 3.6.3 built with Intel Compiler 13.0.079
       a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data

       Use the command:

       module display centos6/netcdf-3.6.3_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/netcdf-4.2.1_intel-13.0.079:

      centos6/netcdf-4.2.1_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       network Common Data Form, version 4.2.1 built with Intel Compiler 13.0.079
       a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data

       Use the command:

       module display centos6/netcdf-4.2.1_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/numpy-1.6.0_python-2.7:

      centos6/numpy-1.6.0_python-2.7
      ****************************************************

       This module sets up the environment for:

       NumPy version 1.6.0, built for python 2.7
       the fundamental package needed for scientific computing with Python

       Use the command:

       module display centos6/numpy-1.6.0_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/numpy-1.7.0_python-2.7.3:

      centos6/numpy-1.7.0_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       NumPy version 1.7.0, built for python 2.7.3
       the fundamental package needed for scientific computing with Python

       Use the command:

       module display centos6/numpy-1.7.0_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Paul Edmon

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/numpy-1.7.1_python-2.7.3:

      centos6/numpy-1.7.1_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       NumPy version 1.7.1, built for python 2.7.3
       the fundamental package needed for scientific computing with Python

       Use the command:

       module display centos6/numpy-1.7.1_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Paul Edmon

      ****************************************************

-------------------------------------------------------------------
updated: 4/19/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/opencv-2.4.4a:

      centos6/opencv-2.4.4a
      ****************************************************

       This module sets up the environment for:

       OpenCV, version OpenCV-2.4.4a
       Open Source Computer Vision -- is a library of programming functions for real time computer vision

       Use the command:

       module display centos6/opencv-2.4.4a

       to see exactly what this module does.

       This module was built by:

       Paul Edmon

      ****************************************************

-------------------------------------------------------------------
updated: 3/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/openmpi-1.6.3_intel-13.0.079:

      centos6/openmpi-1.6.3_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       OpenMPI Version 1.6.3 & Intel 13.0.079 with IB and Thread Support
       OpenMPI package compiled with Intel 13.0.079 version of the Intel Fortran and C compilers, and IDB debugger. This version includes Thread Support.

       Use the command:

       module display centos6/openmpi-1.6.3_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/openmpi-1.6.4_gcc-4.8.0:

      centos6/openmpi-1.6.4_gcc-4.8.0
      ****************************************************

       This module sets up the environment for:

       OpenMPI Version 1.6.4 & GCC 4.8.0 with IB and Thread Support
       OpenMPI package compiled with GCC 4.8.0. This version includes Thread Support.

       Use the command:

       module display centos6/openmpi-1.6.4_gcc-4.8.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/openmpi-1.6.4_intel-13.0.079:

      centos6/openmpi-1.6.4_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       OpenMPI Version 1.6.4 & Intel 13.0.079 with IB and Thread Support
       OpenMPI package compiled with Intel 13.0.079 version of the Intel Fortran and C compilers, and IDB debugger. This version includes Thread Support.

       Use the command:

       module display centos6/openmpi-1.6.4_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/python-2.7.1_full_stack:

      centos6/python-2.7.1_full_stack
      ****************************************************

       This module sets up the environment for:

       Python version 2.7.1, plus lots of extras like numpy, scipy, matplotlib, ipython, etc.
       an interpreted, interactive, object-oriented, extensible programming language

       Use the command:

       module display centos6/python-2.7.1_full_stack

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/python-2.7.1_no_modules:

      centos6/python-2.7.1_no_modules
      ****************************************************

       This module sets up the environment for:

       Python version 2.7.1, without any extra modules
       an interpreted, interactive, object-oriented, extensible programming language

       Use the command:

       module display centos6/python-2.7.1_no_modules

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/python-2.7.3:

      centos6/python-2.7.3
      ****************************************************

       This module sets up the environment for:

       python-2.7.3 module
       Python 2.7.3. This module has been built by Paul Edmon.

       Use the command:

       module display centos6/python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/scipy-0.11.0_python-2.7.3:

      centos6/scipy-0.11.0_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       SciPy version 0.11.0, built for python 2.7.3
       open-source software for mathematics, science, and engineering

       Use the command:

       module display centos6/scipy-0.11.0_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Paul Edmon

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/scipy-0.9.0_python-2.7:

      centos6/scipy-0.9.0_python-2.7
      ****************************************************

       This module sets up the environment for:

       SciPy version 0.9.0, built for python 2.7
       open-source software for mathematics, science, and engineering

       Use the command:

       module display centos6/scipy-0.9.0_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/centos6/shapely-1.2.17_python-2.7.3:

      centos6/shapely-1.2.17_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       SHAPELY 1.2.17
       a Python package for manipulation and analysis of features in the Cartesian plane. This module has been built with Python 2.7.3 by Paul Edmon

       Use the command:

       module display centos6/shapely-1.2.17_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/DMS:

      chem/DMS
      ****************************************************

       This module sets up the environment for:

       DMS
       DMS is an open source program written in C for computing the molecular surface of a molecule.

       Use the command:

       module display chem/DMS

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/06/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/espresso-5.0.2_openmpi-1.6.2_intel-13.0.079:

      chem/espresso-5.0.2_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       Quantum Espresso version 5.0.2
       an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. This module has been built by Plamen G. Krastev.

       Use the command:

       module display chem/espresso-5.0.2_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/22/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/namd-2.7_openmpi-1.4.2_intel-11.1.072:

      chem/namd-2.7_openmpi-1.4.2_intel-11.1.072
      ****************************************************

       This module sets up the environment for:

       NAMD version 2.7 using OpenMPI version 1.4.2
       a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

       Use the command:

       module display chem/namd-2.7_openmpi-1.4.2_intel-11.1.072

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/06/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/namd-2.7b2:

      chem/namd-2.7b2
      ****************************************************

       This module sets up the environment for:

       NAMD version 2.7.b2
       a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

       Use the command:

       module display chem/namd-2.7b2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/07/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/namd-2.7b2_openmpi:

      chem/namd-2.7b2_openmpi
      ****************************************************

       This module sets up the environment for:

       NAMD version 2.7.b2 using OpenMPI
       a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

       Use the command:

       module display chem/namd-2.7b2_openmpi

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/namd-2.7b3_mvapich2-1.5_intel-11.1.072:

      chem/namd-2.7b3_mvapich2-1.5_intel-11.1.072
      ****************************************************

       This module sets up the environment for:

       NAMD version 2.7.b3
       a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

       Use the command:

       module display chem/namd-2.7b3_mvapich2-1.5_intel-11.1.072

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/13/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/nupack3.0:

      chem/nupack3.0
      ****************************************************

       This module sets up the environment for:

       NUPACK version 3.0
       NUPACK is a software suite for the analysis and design of nucleic acid systems. This module has been built by Plamen G. Krastev.

       Use the command:

       module display chem/nupack3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/octopus-3.2.0:

      octopus-3.2.0 module
      ****************************************************

       This module sets up the following environment
       variables for ctopus-3.2.0:
       PATH: /n/sw/octopus-3.2.0/bin
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/openbabel-2.3.0:

      chem/openbabel-2.3.0
      ****************************************************

       This module sets up the environment for:

       Open Babel, version 2.3.0
       Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

       Use the command:

       module display chem/openbabel-2.3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/27/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/orca-2.8_openmpi-1.4.2:

      chem/orca-2.8_openmpi-1.4.2
      ****************************************************

       This module sets up the environment for:

       ORCA 2.8 for OpenMPI 1.4.2
       ORCA modern electron structure program. This binary is for OpenMPI 1.4.2 GNU compiler

       Use the command:

       module display chem/orca-2.8_openmpi-1.4.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/orca-2.9.1_openmpi-1.4.4:

      chem/orca-2.9.1_openmpi-1.4.4
      ****************************************************

       This module sets up the environment for:

       ORCA 2.9.1 for OpenMPI 1.4.4
       ORCA modern electron structure program. This binary is for OpenMPI 1.4.4 GNU compiler. This module has been built by Plamen G. Krastev.

       Use the command:

       module display chem/orca-2.9.1_openmpi-1.4.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/p4vasp-0.3.20:

      chem/p4vasp-0.3.20
      ****************************************************

       This module sets up the environment for:

       p4vasp, version 0.3.20
       A set of tools for processing xml-formatted VASP output

       Use the command:

       module display chem/p4vasp-0.3.20

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/04/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/plumed-1.1.0:

      chem/plumed-1.1.0
      ****************************************************

       This module sets up the environment for:

       PLUMED-1.1.0 using NAMD version 2.7.b1
       PLUMED is a plugin for free energy calculation in molecular systems which works together with some of the most popular molecular dynamics engines. See http://merlino.mi.infn.it/~plumed/PLUMED/Home.html

       Use the command:

       module display chem/plumed-1.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/19/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/sequest.v.27:

      sequest v.27 module
      ****************************************************

       This module sets up the following environment
       variables for sequest:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 1/04/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/turbomole-6.0.2:

      chem/turbomole-6.0.2
      ****************************************************

       This module sets up the environment for:

       TURBOMOLE V6.0.2
       TURBOMOLE V6.0.2

       Use the command:

       module display chem/turbomole-6.0.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/chem/xd2006:

      chem/xd2006
      ****************************************************

       This module sets up the environment for:

       XD2006
       A Computer Program Package for Multipole Refinement, Topological Analysis of Charge Densities and Evaluation of Intermolecular Energies from Experimental and Theoretical Structure Factors

       Use the command:

       module display chem/xd2006

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/22/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/autoconf-2.68:

      devel/autoconf-2.68
      ****************************************************

       This module sets up the environment for:

       autoconf version 2.68
       an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages

       Use the command:

       module display devel/autoconf-2.68

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 7/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/automake-1.11.1:

      devel/automake-1.11.1
      ****************************************************

       This module sets up the environment for:

       automake, version 1.11.1
       Automake is a tool for automatically generating `Makefile.in' files compliant with the GNU Coding Standards.

       Use the command:

       module display devel/automake-1.11.1

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 7/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/charm-6.2:

      devel/charm-6.2
      ****************************************************

       This module sets up the environment for:

       Charm++ ver. 6.2
       Charm++ is a machine independent parallel programming system. Programs written using this system will run unchanged on MIMD machines with or without a shared memory. It provides high-level mechanisms and strategies to facilitate the task of developing even highly complex parallel applications.

       Use the command:

       module display devel/charm-6.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/06/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/cmake-2.6.4:

      devel/cmake-2.6.4
      ****************************************************

       This module sets up the environment for:

       CMake v.2.6.4
       CMake ver. 2.6.4: Compiler

       Use the command:

       module display devel/cmake-2.6.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/09/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/cmake-2.8.1:

      devel/cmake-2.8.1
      ****************************************************

       This module sets up the environment for:

       CMake v.2.8.1
       CMake is a family of tools designed to build, test and package software.

       Use the command:

       module display devel/cmake-2.8.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/26/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/cmake-2.8.8:

      devel/cmake-2.8.8
      ****************************************************

       This module sets up the environment for:

       CMake v.2.8.8
       CMake is a family of tools designed to build, test and package software. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/cmake-2.8.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/29/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/ddt:

      devel/ddt
      ****************************************************

       This module sets up the environment for:

       DDT
       Set up the environment for the DDT Debugger

       Use the command:

       module display devel/ddt

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/04/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/ddt3.2:

      devel/ddt3.2
      ****************************************************

       This module sets up the environment for:

       DDT
       Set up the environment for the DDT 3.2 Debugger

       Use the command:

       module display devel/ddt3.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/27/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/drmaa-python-0.4b2:

      devel/drmaa-python-0.4b2
      ****************************************************

       This module sets up the environment for:

       DRMAA Python version 0.4b2
       a python package to interact with DRMAA-compliant distributed resource management systems

       Use the command:

       module display devel/drmaa-python-0.4b2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/25/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/dropbox:

      devel/dropbox
      ****************************************************

       This module sets up the environment for:

       Dropbox
       Dropbox allows you to sync your files online and across your computers automatically.

       Use the command:

       module display devel/dropbox

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/23/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/ec2cmd:

      devel/ec2cmd
      ****************************************************

       This module sets up the environment for:

       ec2cmd svn trunk
       Command line tools to connect to Amazon EC2

       Use the command:

       module display devel/ec2cmd

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/13/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/electric-fence-2.1.13:

      devel/electric-fence-2.1.13
      ****************************************************

       This module sets up the environment for:

       electricfence-2.1.13
       A malloc() debugger for Linux and Unix. This will stop your program on the exact instruction that overruns or under-runs a malloc() buffer.

       Use the command:

       module display devel/electric-fence-2.1.13

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/19/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/flex-2.5.33:

      devel/flex-2.5.33
      ****************************************************

       This module sets up the environment for:

       flex version 2.5.33
       Flex is a fast lexical analyzer generator. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/flex-2.5.33

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/fltk-1.3.x-r6916:

      devel/fltk-1.3.x-r6916
      ****************************************************

       This module sets up the environment for:

       Fast Light Toolkit Version fltk-1.3.x
       FLTK is a cross-platform C++ GUI toolkit

       Use the command:

       module display devel/fltk-1.3.x-r6916

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/19/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/fuse-2.7.4:

      devel/fuse-2.7.4
      ****************************************************

       This module sets up the environment for:

       fuse v.2.7.4
       With FUSE it is possible to implement a fully functional filesystem in a userspace program

       Use the command:

       module display devel/fuse-2.7.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/01/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/gcc-4.3.5:

      devel/gcc-4.3.5
      ****************************************************

       This module sets up the environment for:

       GNU Compiler Collection version 4.3.5
       includes C, C++, and Fortran

       Use the command:

       module display devel/gcc-4.3.5

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/gdata-2.0.10_python-2.7.3:

      devel/gdata-2.0.10_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       gdata version 2.0.10
       The Google Data APIs (Google Data) provide a simple protocol for reading and writing data on the web. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/gdata-2.0.10_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/09/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/gperf-3.0.4:

      devel/gperf-3.0.4
      ****************************************************

       This module sets up the environment for:

       gperf v. 3.0.4
       GNU gperf is a perfect hash function generator

       Use the command:

       module display devel/gperf-3.0.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/guile-1.8.7:

      devel/guile-1.8.7
      ****************************************************

       This module sets up the environment for:

       guile version 1.8.7
       guile version 1.8.7

       Use the command:

       module display devel/guile-1.8.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/18/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/harminv-1.3.1:

      devel/harminv-1.3.1
      ****************************************************

       This module sets up the environment for:

       harminv (intel) version 1.3.1
       harminv (intel) version 1.3.1

       Use the command:

       module display devel/harminv-1.3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/18/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/hypre-2.0.0_openmpi-1.3.3_intel-11.1.046:

      devel/hypre-2.0.0_openmpi-1.3.3_intel-11.1.046
      ****************************************************

       This module sets up the environment for:

       HYPRE, compiled with the openmpi-1.3.3_intel-11.1.046 suite
       HYPRE high performance preconditioners, compiled with the openmpi-1.3.3_intel-11.1.046 suite

       Use the command:

       module display devel/hypre-2.0.0_openmpi-1.3.3_intel-11.1.046

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/04/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/igraph-0.5.3:

      devel/igraph-0.5.3
      ****************************************************

       This module sets up the environment for:

       igraph 0.5.3
       igraph is a free software package for creating and manipulating undirected and directed graphs.

       Use the command:

       module display devel/igraph-0.5.3

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 4/07/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intel-11.1.046:

      devel/intel-11.1.046
      ****************************************************

       This module sets up the environment for:

       Intel Compilers Version 11.1.046
       Intel Fortran and C compilers, and IDB debugger, Version 11.1.046

       Use the command:

       module display devel/intel-11.1.046

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intel-11.1.072:

      devel/intel-11.1.072
      ****************************************************

       This module sets up the environment for:

       Intel Compilers Version 11.1.072
       Intel Fortran and C compilers, and IDB debugger, Version 11.1.072

       Use the command:

       module display devel/intel-11.1.072

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/11/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intel-2011.2.137:

      devel/intel-2011.2.137
      ****************************************************

       This module sets up the environment for:

       Intel Compilers (Composer CE) Version 2011.2.137
       Intel Fortran and C compilers, and IDB debugger (Composer XE), Version 2011.2.137

       Use the command:

       module display devel/intel-2011.2.137

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intel-2011.2.137_32bit:

      devel/intel-2011.2.137_32bit
      ****************************************************

       This module sets up the environment for:

       Intel Compilers (Composer CE) Version 2011.2.137
       Intel Fortran and C compilers, and IDB debugger (Composer XE), Version 2011.2.137

       Use the command:

       module display devel/intel-2011.2.137_32bit

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/19/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intel-and-mkl-12.3.174:

      devel/intel-and-mkl-12.3.174
      ****************************************************

       This module sets up the environment for:

       Intel Compilers and MKL Version 12.3.174
       Intel Fortran and C compilers, and IDB debugger, and MKL suite Version 12.3.174

       Use the command:

       module display devel/intel-and-mkl-12.3.174

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/intltool-0.40.6:

      devel/intltool-0.40.6
      ****************************************************

       This module sets up the environment for:

       The intltool package contains an internationalization tool
       Intltool v.0.40.6

       Use the command:

       module display devel/intltool-0.40.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/io_lib:

      devel/io_lib
      ****************************************************

       This module sets up the environment for:

       IO_LIB v.1.12.5
       Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface

       Use the command:

       module display devel/io_lib

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/io_lib_old:

      devel/io_lib_old
      ****************************************************

       This module sets up the environment for:

       IO_LIB v.1.12.1
       Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface

       Use the command:

       module display devel/io_lib_old

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/14/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/libAWS-0.9.2:

      devel/libAWS-0.9.2
      ****************************************************

       This module sets up the environment for:

       libAWS v.0.9.2
       A C++ Library for Interfacing with Amazon Web Services

       Use the command:

       module display devel/libAWS-0.9.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/01/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/libctl-3.1:

      devel/libctl-3.1
      ****************************************************

       This module sets up the environment for:

       libctl (intel) version 3.1
       libctl (intel) version 3.1

       Use the command:

       module display devel/libctl-3.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/17/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/libgnomecanvas-2.26.0:

      devel/libgnomecanvas-2.26.0
      ****************************************************

       This module sets up the environment for:

       libgnomecanvas version 2.26.0
       libgnomecanvas version 2.26.0

       Use the command:

       module display devel/libgnomecanvas-2.26.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/libgnomeui-2.18.1:

      devel/libgnomeui-2.18.1
      ****************************************************

       This module sets up the environment for:

       libgnomeui version 2.18.1
       libgnomeui version 2.18.1

       Use the command:

       module display devel/libgnomeui-2.18.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/librsync-0.9.7:

      devel/librsync-0.9.7
      ****************************************************

       This module sets up the environment for:

       librsync version 0.9.7
       a free software library that implements the rsync remote-delta algorithm

       Use the command:

       module display devel/librsync-0.9.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/05/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/libtool-2.4:

      devel/libtool-2.4
      ****************************************************

       This module sets up the environment for:

       libtool version 2.4
       GNU libtool is a generic library support script.

       Use the command:

       module display devel/libtool-2.4

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 7/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/lsf_drmaa-1.0.3:

      devel/lsf_drmaa-1.0.3
      ****************************************************

       This module sets up the environment for:

       FedStage DRMAA for LSF, version 1.0.3
       an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource Management Application API) specification for the submission and control of jobs to Platform LSF

       Use the command:

       module display devel/lsf_drmaa-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/lsf_drmaa-1.0.3-debug:

      devel/lsf_drmaa-1.0.3-debug
      ****************************************************

       This module sets up the environment for:

       FedStage DRMAA for LSF, version 1.0.3
       an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource Management Application API) specification for the submission and control of jobs to Platform LSF

       Use the command:

       module display devel/lsf_drmaa-1.0.3-debug

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/02/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/lsf_drmaa-1.0.4:

      devel/lsf_drmaa-1.0.4
      ****************************************************

       This module sets up the environment for:

       FedStage DRMAA for LSF, version 1.0.4
       an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource Management Application API) specification for the submission and control of jobs to Platform LSF. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/lsf_drmaa-1.0.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mercurial-1.8.3:

      devel/mercurial-1.8.3
      ****************************************************

       This module sets up the environment for:

       mercurial, version 1.8.3
       a distributed version control system

       Use the command:

       module display devel/mercurial-1.8.3

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 5/11/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mercurial-2.0.1:

      devel/mercurial-2.0.1
      ****************************************************

       This module sets up the environment for:

       mercurial, version 2.0.1
       a distributed version control system

       Use the command:

       module display devel/mercurial-2.0.1

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 12/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mercurial-2.2.3_python-2.6_no-autoload-python:

      devel/mercurial-2.2.3_python-2.6_no-autoload-python
      ****************************************************

       This module sets up the environment for:

       Mercurial version 2.2.3, built for python 2.6 but doesn't autoload any dependencies
       a free, distributed source control management tool

       Use the command:

       module display devel/mercurial-2.2.3_python-2.6_no-autoload-python

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 7/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mercurial-2.2.3_python-2.7_no-autoload-python:

      devel/mercurial-2.2.3_python-2.7_no-autoload-python
      ****************************************************

       This module sets up the environment for:

       Mercurial version 2.2.3, built for python 2.6 but doesn't autoload any dependencies
       a free, distributed source control management tool

       Use the command:

       module display devel/mercurial-2.2.3_python-2.7_no-autoload-python

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mono-2.10.8:

      devel/mono-2.10.8
      ****************************************************

       This module sets up the environment for:

       Mono version 2.10.8
       A software platform designed to allow developers to easily create cross platform applications. This module has been built by Plamen G. Krastev

       Use the command:

       module display devel/mono-2.10.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/18/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/mono-2.6.1:

      devel/mono-2.6.1
      ****************************************************

       This module sets up the environment for:

       Mono is a software platform designed to allow developers to easily create cross platform applications.
       Mono platform v. 2.6.1

       Use the command:

       module display devel/mono-2.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/openexr-1.6.1_intel-11.0.083:

      devel/openexr-1.6.1_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       OpenEXR v1.6.1 and ILMBase v1.0.1
       OpenEXR v1.6.1 and ILMBase v1.0.1 -- OpenEXR is a high dynamic-range (HDR) image file format

       Use the command:

       module display devel/openexr-1.6.1_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/11/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/pgi-11.8:

      devel/pgi-11.8
      ****************************************************

       This module sets up the environment for:

       PGI compiler 11.8
       Portland PGI compilter for x86_64.

       Use the command:

       module display devel/pgi-11.8

       to see exactly what this module does.

       This module was built by:

       methier

      ****************************************************

-------------------------------------------------------------------
updated: 9/23/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/pvm-3.4.6:

      devel/pvm-3.4.6
      ****************************************************

       This module sets up the environment for:

       PVM v.3.4.6
       PVM (Parallel Virtual Machine) is a software package that permits a heterogeneous collection of Unix and/or Windows computers hooked together by a network to be used as a single large parallel computer

       Use the command:

       module display devel/pvm-3.4.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/22/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/pylsf-0.0.1-patched:

      devel/pylsf-0.0.1-patched
      ****************************************************

       This module sets up the environment for:

       PyLSF version 0.0.1 (2009-02-23)
       a Python/Pyrex module to allow access to the version 6.2 of Platform HPC LSF batch scheduler

       Use the command:

       module display devel/pylsf-0.0.1-patched

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/03/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/pyrex-0.9.8.5:

      devel/pyrex-0.9.8.5
      ****************************************************

       This module sets up the environment for:

       Pyrex version 0.9.8.5
       a language for writing python extension modules

       Use the command:

       module display devel/pyrex-0.9.8.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/03/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/rpy-1.0.3:

      devel/rpy-1.0.3
      ****************************************************

       This module sets up the environment for:

       RPy version 1.0.3
       RPy is a very simple, yet robust, Python interface to the R Programming Language

       Use the command:

       module display devel/rpy-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/04/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/rpy2-2.1.7:

      devel/rpy2-2.1.7
      ****************************************************

       This module sets up the environment for:

       RPy version 2.1.7
       RPy is a very simple, yet robust, Python interface to the R Programming Language

       Use the command:

       module display devel/rpy2-2.1.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/03/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/s3cmd:

      devel/s3cmd
      ****************************************************

       This module sets up the environment for:

       s3cmd svn trunk
       Command line tools to connect to Amazon S3

       Use the command:

       module display devel/s3cmd

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/03/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/tcl-8.4.18:

      devel/tcl-8.4.18
      ****************************************************

       This module sets up the environment for:

       Tcl version 8.4.18
       Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/tcl-8.4.18

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/tclap-1.1.0:

      devel/tclap-1.1.0
      ****************************************************

       This module sets up the environment for:

       TClap v.1.1.0
       TClap version 1.1.0 -- C++ command line parser

       Use the command:

       module display devel/tclap-1.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/09/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/tk-8.4.18:

      devel/tk-8.4.18
      ****************************************************

       This module sets up the environment for:

       Tk version 8.4.18
       Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/tk-8.4.18

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/totalview-8.8.0-1:

      devel/totalview-8.8.0-1
      ****************************************************

       This module sets up the environment for:

       Totalview v.8.8.0-1
       Dynamic source code and memory debugging for C, C++ and Fortran applications

       Use the command:

       module display devel/totalview-8.8.0-1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/04/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/valgrind-3.6.1:

      devel/valgrind-3.6.1
      ****************************************************

       This module sets up the environment for:

       Valgrind Version 3.6.1
       Valgrind is an instrumentation framework for building dynamic analysis tools.

       Use the command:

       module display devel/valgrind-3.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/vtune-9.1:

      devel/vtune-9.1
      ****************************************************

       This module sets up the environment for:

       Intel Vtune v. 9.1
       Intel VTune Performance Analyzer evaluates applications on all sizes of systems based on Intel processors

       Use the command:

       module display devel/vtune-9.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/wine-1.4.1:

      devel/wine-1.4.1
      ****************************************************

       This module sets up the environment for:

       wine version 1.4.1
       a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD. This module has been built by Plamen G. Krastev.

       Use the command:

       module display devel/wine-1.4.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/wxPython-2.8.10.1:

      devel/wxPython-2.8.10.1
      ****************************************************

       This module sets up the environment for:

       wxPython version 2.8.10.1
       a GUI toolkit for the Python programming language

       Use the command:

       module display devel/wxPython-2.8.10.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/wxWidgets-2.8.10:

      devel/wxWidgets-2.8.10
      ****************************************************

       This module sets up the environment for:

       wxWidgets
       a cross-platform GUI and tools library

       Use the command:

       module display devel/wxWidgets-2.8.10

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/19/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/wxWidgets-2.8.10.orig:

      devel/wxWidgets-2.8.10.orig
      ****************************************************

       This module sets up the environment for:

       wxWidgets v2.8.10
       A widget toolkit for creating graphical user interfaces

       Use the command:

       module display devel/wxWidgets-2.8.10.orig

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/19/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/wxWidgets-2.9.4:

      devel/wxWidgets-2.9.4
      ****************************************************

       This module sets up the environment for:

       wxWidgets 2.9.4
       a cross-platform GUI and tools library

       Use the command:

       module display devel/wxWidgets-2.9.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/xemacs-21.5.29:

      devel/xemacs-21.5.29
      ****************************************************

       This module sets up the environment for:

       Xemacs
       Xemacs editor

       Use the command:

       module display devel/xemacs-21.5.29

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/29/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/yaml-0.1.3:

      devel/yaml-0.1.3
      ****************************************************

       This module sets up the environment for:

       YAML libs, version 0.1.3
       YAML libraries, version 0.1.3

       Use the command:

       module display devel/yaml-0.1.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/01/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/devel/zsh-4.3.14:

      devel/zsh-4.3.14
      ****************************************************

       This module sets up the environment for:

       zsh shell - version 4.3.14
       Z shell

       Use the command:

       module display devel/zsh-4.3.14

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 12/12/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/GMT4.5.5:

      geo/GMT4.5.5
      ****************************************************

       This module sets up the environment for:

       GMT v.4.5.5
       GMT is Generic Mapping Tools

       Use the command:

       module display geo/GMT4.5.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/bufr_000381:

      geo/bufr_000381
      ****************************************************

       This module sets up the environment for:

       BUFRDC library version 000381
       BUFRDC library

       Use the command:

       module display geo/bufr_000381

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/09/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/gdal-1.6.1:

      geo/gdal-1.6.1
      ****************************************************

       This module sets up the environment for:

       GDAL v.1.6.1
       GDAL is a translator library for raster geospatial data formats

       Use the command:

       module display geo/gdal-1.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/08/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/gdal-1.7.2:

      geo/gdal-1.7.2
      ****************************************************

       This module sets up the environment for:

       GDAL v.1.7.2
       GDAL is a translator library for raster geospatial data formats

       Use the command:

       module display geo/gdal-1.7.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/18/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/grass-6.4.0RC5:

      geo/grass-6.4.0RC5
      ****************************************************

       This module sets up the environment for:

       GRASS v.6.4.0RC5
       Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization

       Use the command:

       module display geo/grass-6.4.0RC5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/08/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/ioapi-3.0:

      geo/ioapi-3.0
      ****************************************************

       This module sets up the environment for:

       I/O API library, version 3.0
       A cartographical projection program

       Use the command:

       module display geo/ioapi-3.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/23/2010

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/geo/proj-4.6.1:

      geo/proj-4.6.1
      ****************************************************

       This module sets up the environment for:

       Proj v.4.6.1
       A cartographical projection program

       Use the command:

       module display geo/proj-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/08/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Ampac:

      Ampac module
      ****************************************************

       This module sets up the following environment
       variables for Ampac:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/BayesPhylogenies:

      hpc/BayesPhylogenies
      ****************************************************

       This module sets up the environment for:

       BayesPhylogenies
       BayesPhylogenies: For inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo

       Use the command:

       module display hpc/BayesPhylogenies

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/C++QED:

      hpc/C++QED
      ****************************************************

       This module sets up the environment for:

       C++QED
       a highly flexible framework for simulating open quantum dynamics. It allows users to build arbitrarily complex interacting quantum systems from elementary free subsystems and interactions, and simulate their time evolution with a number of available time-evolution drivers. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/C++QED

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/CitcomS-3.1.1:

      hpc/CitcomS-3.1.1
      ****************************************************

       This module sets up the environment for:

       CitcomS-3.1.1
       CitcomS is a finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.

       Use the command:

       module display hpc/CitcomS-3.1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 11/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/CitcomS-3.1.1_Moucha:

      hpc/CitcomS-3.1.1_Moucha
      ****************************************************

       This module sets up the environment for:

       CitcomS-3.1.1_Moucha
       CitcomS is a finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.

       Use the command:

       module display hpc/CitcomS-3.1.1_Moucha

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Cython-0.14.1:

      hpc/Cython-0.14.1
      ****************************************************

       This module sets up the environment for:

       Cython-0.14.1, C Extensions for Python
       Cython-0.14.1, C Extensions for Python

       Use the command:

       module display hpc/Cython-0.14.1

       to see exactly what this module does.

       This module was built by:

       Matthew Nicholson

      ****************************************************

-------------------------------------------------------------------
updated: 3/25/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/DendroPy-3.12.0_python-2.7.3:

      hpc/DendroPy-3.12.0_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       DendroPy version 3.12.0, built for python 2.7.3
       A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters

       Use the command:

       module display hpc/DendroPy-3.12.0_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 2/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/EMBOSS-6.4.0:

      emboss module
      ****************************************************

       This module sets up the following environment
       variables for emboss:
       PATH /n/sw/EMBOSS-6.4.0/bin
       PLPLOT_LIB /n/sw/EMBOSS-6.4.0/lib
       emboss_acdroot /n/sw/EMBOSS-6.4.0/share/EMBOSS/acd

      ****************************************************

-------------------------------------------------------------------
updated: 3/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ESMF_3_1_0rp2:

      hpc/ESMF_3_1_0rp2
      ****************************************************

       This module sets up the environment for:

       Earth System Modeling Framework (ESMF) v3.1.0rp2 using Openmpi 1.2.5 and Intel Compilers
       Earth System Modeling Framework (ESMF) v3.1.0rp2 using Openmpi 1.2.5 Intel Compilers

       Use the command:

       module display hpc/ESMF_3_1_0rp2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/GAPipeline-0.3.0:

      GAPipeline-0.3.0 module
      ****************************************************

       This module sets up the following environment
       variables for GAPipeline-0.3.0:
       PATH /n/sw/odyssey-apps/GAPipeline-0.3.0/Goat

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/GAPipeline-1.5.1:

      hpc/GAPipeline-1.5.1
      ****************************************************

       This module sets up the environment for:

       GAPipeline-1.5.1
       Solexa pipeline, version 1.5.1

       Use the command:

       module display hpc/GAPipeline-1.5.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/GDL-0.9:

      hpc/GDL-0.9
      ****************************************************

       This module sets up the environment for:

       GDL vers. 0.9rc2
       GDL version 0.9rc2 compiled with Intel 10.1.018

       Use the command:

       module display hpc/GDL-0.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/IDL-7.0:

      IDL module
      ****************************************************

       This module sets up the following environment
       variables for IDL version 7.0:
       PATH IDL_PATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/IDL-7.1:

      IDL module
      ****************************************************

       This module sets up the following environment
       variables for IDL version 7.1:
       PATH IDL_PATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/IDL_AstroLib:

      hpc/IDL_AstroLib
      ****************************************************

       This module sets up the environment for:

       IDL Astronomy Library
       The IDL Astronomy Users Library is a central repository for low-level astronomy software written in the commercial language IDL. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/IDL_AstroLib

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/IFrIT-3.2.5:

      IFrIT module
      ****************************************************

       This module sets up the following environment
       variables for IFrIT version 3.2.5:
       PATH
       QTDIR

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/JAGS-1.0.3:

      hpc/JAGS-1.0.3
      ****************************************************

       This module sets up the environment for:

       JAGS (Just Another Gibbs Sampler) version 1.0.3
       JAGS is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation

       Use the command:

       module display hpc/JAGS-1.0.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/LiE:

      hpc/LiE
      ****************************************************

       This module sets up the environment for:

       LiE
       a computer algebra package for lie group computations

       Use the command:

       module display hpc/LiE

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/MACS-1.4.0:

      MACS module
      ****************************************************

       This module sets up the following environment
       variables for MACS version 1.4.0alpha2:
       PATH
       MANPATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/MMTK-2.7.5:

      hpc/MMTK-2.7.5
      ****************************************************

       This module sets up the environment for:

       Molecular Modelling Toolkit (MMTK)
       MMTK is an Open Source program library for molecular simulation applications. This module has been built with Python 2.7.1, HDF5 1.8.6, and netCDF 4.2 by Plamen G. Krastev.

       Use the command:

       module display hpc/MMTK-2.7.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/MUMmer3.20:

MUMmer3.20 module
      ****************************************************

       This module sets up the following environment
       variables for MUMmer3.20:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/MUMmer3.22:

MUMmer3.22 module
      ****************************************************

       This module sets up the following environment
       variables for MUMmer3.22:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 5/04/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Macaulay2-1.1:

      hpc/Macaulay2-1.1
      ****************************************************

       This module sets up the environment for:

       Macaulay2 version 1.1
       algebraic geometry and commutative algebra software

       Use the command:

       module display hpc/Macaulay2-1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/MatlabMPI-1.2:

      hpc/MatlabMPI-1.2
      ****************************************************

       This module sets up the environment for:

       MatlabMPI version 1.2
       MatlabMPI is set of Matlab scripts that implement a subset of MPI and allow any Matlab program to be run on a parallel computer. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/MatlabMPI-1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/OpenSceneGraph-2.8.2:

      hpc/OpenSceneGraph-2.8.2
      ****************************************************

       This module sets up the environment for:

       OpenSceneGraph version 2.8.2
       The OpenSceneGraph is an open source high performance 3D graphics toolkit, used by application developers in fields such as visual simulation, games, virtual reality, scientific visualization and modelling. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/OpenSceneGraph-2.8.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/22/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Perl-Parallel-MPI-Simple-0.03:

      hpc/Perl-Parallel-MPI-Simple-0.03
      ****************************************************

       This module sets up the environment for:

       Parallel-MPI-Simple-0.03
       Perl module standalone called Parallel-MPI-Simple-0.03

       Use the command:

       module display hpc/Perl-Parallel-MPI-Simple-0.03

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/28/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Perl_Parallel_MPI-0.03:

      hpc/Perl_Parallel_MPI-0.03
      ****************************************************

       This module sets up the environment for:

       Perl MPI version0.03
       This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/Perl_Parallel_MPI-0.03

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/01/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/Pmw-1.3.2_python-2.7.1:

      hpc/Pmw-1.3.2_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       Pmw
       A toolkit for building high-level compound widgets in Python using the Tkinter module. This module was built with Python 2.7.1 by Plamen G Krastev.

       Use the command:

       module display hpc/Pmw-1.3.2_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/PyOpenGL-3.0_python-2.7.1:

      hpc/PyOpenGL-3.0_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       PyOpenGL
       Cross platform Python binding to OpenGL and related APIs. This module was built with Python 2.7.1 by Plamen G Krastev.

       Use the command:

       module display hpc/PyOpenGL-3.0_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/28/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/PyYAML-3.10_python-2.7:

      hpc/PyYAML-3.10_python-2.7
      ****************************************************

       This module sets up the environment for:

       PyYAML version 3.10, built for python 2.7
       a YAML parser and emitter for Python

       Use the command:

       module display hpc/PyYAML-3.10_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 11/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/R-2.7.1:

      R module
      ****************************************************

       This module sets up the following environment
       variables for R version 2.7.1:
       PATH
       MANPATH
       LD_LIBRARY_PATH (required by packages)

       For questions or package requests, contact
       rchelp@fas.harvard.edu
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/R-2.9.0:

      hpc/R-2.9.0
      ****************************************************

       This module sets up the environment for:

       R-2.9.0
       R project for statistical computing, version 2.9.0 (4/17/09)

       Use the command:

       module display hpc/R-2.9.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/RAxML-7.0.4:

      RAxML

      ****************************************************

       This module sets up the following environment
       variables for RAxML:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/RAxML-7.0.4_MPI:

      raxmlHPC-MPI

      ****************************************************

       This module sets up the following environment
       variables for raxmlHPC-MPI:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/SAGA-GIS-2.0:

      hpc/SAGA-GIS-2.0
      ****************************************************

       This module sets up the environment for:

       SAGA GIS 2.0
       SAGA GIS 2.0

       Use the command:

       module display hpc/SAGA-GIS-2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/SCM-5e7:

      hpc/SCM-5e7
      ****************************************************

       This module sets up the environment for:

       SCM, Version 5e7
       SCM is a portable Scheme implementation written in C

       Use the command:

       module display hpc/SCM-5e7

       to see exactly what this module does.

       This module was built by:

       methier

      ****************************************************

-------------------------------------------------------------------
updated: 4/05/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/SWarp/default:

      SWarp module
      ****************************************************

       This module sets up the following environment
       variables for SWarp:
       PATH
       MANPATH
       SWARP_VERSION

       Version 2.17.1

      ****************************************************

-------------------------------------------------------------------
updated: 3/30/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/SWarp/swarp_2.17.1:

      SWarp module
      ****************************************************

       This module sets up the following environment
       variables for SWarp:
       PATH
       MANPATH
       SWARP_VERSION

       Version 2.17.1

      ****************************************************

-------------------------------------------------------------------
updated: 3/30/2009

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ScientificPython-2.9.1_python-2.7:

      hpc/ScientificPython-2.9.1_python-2.7
      ****************************************************

       This module sets up the environment for:

       ScientificPython version 2.9.1
       a Python library for common tasks in scientific computing (independent of SciPy)

       Use the command:

       module display hpc/ScientificPython-2.9.1_python-2.7

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 5/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/TMHMM2.0c:

      hpc/TMHMM2.0c
      ****************************************************

       This module sets up the environment for:

       TMHMM2.0c
       prediction of transmembrane helices in proteins

       Use the command:

       module display hpc/TMHMM2.0c

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/VelvetOptimiser-2.2.0:

      hpc/VelvetOptimiser-2.2.0
      ****************************************************

       This module (max kmer=70) sets up the environment for:

       VelvetOptimiser-2.2.0 velvet_1.1.03 max kmer=70
       VelvetOptimiser is a multi-threaded Perl script for automatically optimising the parameter options for the Velvet de novo sequence assembler.

       Use the command:

       module display hpc/VelvetOptimiser-2.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/17/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/abinit-6.0.4:

      abinit-6.0.4 Module
      ****************************************************

       This module sets up the following environment
       variables for abinit-6.0.4:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/abinit-6.8.1:

      abinit-6.8.1 Module
      ****************************************************

       This module sets up the following environment
       variables for abinit-6.8.1:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 7/27/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/abyss-1.1.2:

      hpc/abyss-1.1.2
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.1.2
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

       Use the command:

       module display hpc/abyss-1.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/abyss-1.2.1:

      hpc/abyss-1.2.1
      ****************************************************

       This module sets up the environment for:

       ABySS version 1.2.1
       ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.

       Use the command:

       module display hpc/abyss-1.2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/adda-1.1_openmpi-1.6.2_intel-13.0.079:

      hpc/adda-1.1_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       ADDA version 1.1
       a C software package to calculate scattering and absorption of electromagnetic waves by particles of arbitrary shape and composition using the discrete dipole approximation (DDA). This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/adda-1.1_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/18/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/anaconda-1.5.0:

      hpc/anaconda-1.5.0
      ****************************************************

       This module sets up the environment for:

       Anaconda version 1.5.0
       an enterprise-ready Python distribution for large-scale data processing, predictive analytics, and scientific computing. This module has been built by Plamen G Krastev.

       Use the command:

       module display hpc/anaconda-1.5.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/antlr-2.7.7:

      hpc/antlr-2.7.7
      ****************************************************

       This module sets up the environment for:

       antlr version 2.7.7
       ANother Tool for Language Recognition, version 2.7.7

       Use the command:

       module display hpc/antlr-2.7.7

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/19/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/apache-ant-1.8.1:

      hpc/apache-ant-1.8.1
      ****************************************************

       This module sets up the environment for:

       Apache ANT 1.8.1
       Apache ANT 1.8.1

       Use the command:

       module display hpc/apache-ant-1.8.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/aspera:

      hpc/aspera
      ****************************************************

       This module sets up the environment for:

       aspera ascp
       Aspera is a commercial file transfer protocol that provides better transfer speeds than ftp over long distances. For short distance file transfers we continue to recommend the use of ftp

       Use the command:

       module display hpc/aspera

       to see exactly what this module does.
Your command should look similar to this:
ascp -QT -l 300m -i <aspera connect installation directory>/etc/asperaweb_id_dsa.putty era-fasp@fasp.sra.ebi.ac.uk:<file or files to download> <download location>
Single file download:
ascp -QT -l 300m -i /etc/aperaweb_id_dsa.putty era-fasp@fasp.sra.ebi.ac.uk:/vol1/ERA012/ERA012008/sff/library08_GJ6U61T06.sff /.
Multiple file download:
ascp -QT -l 300m -i /etc/aperaweb_id_dsa.putty era-fasp@fasp.sra.ebi.ac.uk:/vol1/ERA012/ERA012008/sff/ /.
      ****************************************************

-------------------------------------------------------------------
updated: 2/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/astrometry.net-0.40:

      hpc/astrometry.net-0.40
      ****************************************************

       This module sets up the environment for:

       Astrometry.net 0.40
       Astrometry.net 0.40

       Use the command:

       module display hpc/astrometry.net-0.40

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/22/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/astron-2010.11.19:

      hpc/astron-2010.11.19
      ****************************************************

       This module sets up the environment for:

       The IDL Astronomy User's Library
       a central repository for general purpose astronomy procedures written in IDL

       Use the command:

       module display hpc/astron-2010.11.19

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/atk-1.28.0:

      hpc/atk-1.28.0
      ****************************************************

       This module sets up the environment for:

       atk version 1.28.0
       accessibility toolkit for GNOME

       Use the command:

       module display hpc/atk-1.28.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/atlas3.2:

      hpc/atlas3.2
      ****************************************************

       This module sets up the environment for:

       ATLAS ver. 3.2
       ATLAS optimized BLAS routines ver. 3.2

       Use the command:

       module display hpc/atlas3.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/augustus-2.1:

      hpc/augustus-2.1
      ****************************************************

       This module sets up the environment for:

       AUGUSTUS version 2.1
       a program that predicts genes in eukaryotic genomic sequences

       Use the command:

       module display hpc/augustus-2.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/autoconf-2.63:

      hpc/autoconf-2.63
      ****************************************************

       This module sets up the environment for:

       autoconf version 2.63
       an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages

       Use the command:

       module display hpc/autoconf-2.63

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/azove-2.0:

      hpc/azove-2.0
      ****************************************************

       This module sets up the environment for:

       azove, version 2.0
       azove-2.0, is a tool designed for counting (without explicit enumeration) and enumeration of 0/1 vertices.

       Use the command:

       module display hpc/azove-2.0

       to see exactly what this module does.

       This module was built by:

       methier

      ****************************************************

-------------------------------------------------------------------
updated: 9/07/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bbcp:

      hpc/bbcp
      ****************************************************

       This module sets up the environment for:

       bbcp
       bbcp File Transfer Program

       Use the command:

       module display hpc/bbcp

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bd_box-1.1:

      hpc/bd_box-1.1
      ****************************************************

       This module sets up the environment for:

       BD_BOX version 1.1
       BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/bd_box-1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/17/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/beast:

      Beast module
      ****************************************************

       This module sets up the following environment
       variables for Beast:
       PATH /n/sw/odyssey-apps/beast-1.4.7/bin

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/beast-1.4.8:

      hpc/beast-1.4.8
      ****************************************************

       This module sets up the environment for:

       BEAST version 1.4.8
       Bayesian Evolutionary Analysis Sampling Trees

       Use the command:

       module display hpc/beast-1.4.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/beast-1.6.1:

      hpc/beast-1.6.1
      ****************************************************

       This module sets up the environment for:

       BEAST version 1.6.1
       Bayesian Evolutionary Analysis Sampling Trees

       Use the command:

       module display hpc/beast-1.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/beautifulsoup4-4.1.3_python-2.7.1:

      hpc/beautifulsoup4-4.1.3_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       Beautiful Soup version 4.1.3
       Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/beautifulsoup4-4.1.3_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/18/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/best-2.3_openmpi-1.3.2_intel-11.0.083:

      hpc/best-2.3_openmpi-1.3.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       BEST version 3.2 with MPI support
       Bayesian Estimation of Species Trees

       Use the command:

       module display hpc/best-2.3_openmpi-1.3.2_intel-11.0.083

       to see exactly what this module does.

       This build includes patches described at
       http://www.bestgrid.org/index.php/Bioinformatics_applications_at_University_of_Canterbury_HPC#Installing_MrBayes
       o fix for problem with SumP hanging in MPI on error
       o fix minor issue in mcmcdiagn param print
       o fix for 64-bit architecture
       plus a custom FAS IT RC patch
       o fix to not use readline when stdin is not a tty


      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/best2:

      best2 module
      ****************************************************

       This module sets up the following environment
       variables for best2:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/best23:

      hpc/best23
      ****************************************************

       This module sets up the environment for:

       BEST23
       BEST23: Bayesian Best version 2.2: updated. Serial version is best23 and OpenMPI version is best23_mpi.

       Use the command:

       module display hpc/best23

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/best24:

      hpc/best24
      ****************************************************

       This module sets up the environment for:

       BEST24
       BEST24: Bayesian Best version 2.4: updated. Serial version is best24.

       Use the command:

       module display hpc/best24

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/best_paral:

      hpc/best_paral
      ****************************************************

       This module sets up the environment for:

       best_paral
       Best_paral - compiled with openmpi-1.4.2_gnu-4.1.2 and gcc-4.3.3

       Use the command:

       module display hpc/best_paral

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bioperl-1.5.2_102:

      hpc/bioperl-1.5.2_102
      ****************************************************

       This module sets up the environment for:

       BioPerl version 1.5.2_102
       open source Perl tools for bioinformatics, genomics and life science

       Use the command:

       module display hpc/bioperl-1.5.2_102

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/biopython-1.58_python-2.7.1:

      hpc/biopython-1.58_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       Biopython Version 1.58
       Biopython is a set of freely available tools for biological computation written in Python

       Use the command:

       module display hpc/biopython-1.58_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/05/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/biopython-1.60_python-2.7.3:

      hpc/biopython-1.60_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       Biopython Version 1.60
       Biopython is a set of freely available tools for biological computation written in Python

       Use the command:

       module display hpc/biopython-1.60_python-2.7.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/26/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/blastall:

      NCBI Blast module (blastall)
      ****************************************************

       This module sets up the following environment
       variables for NCBI Blast (blastall command):
       PATH /n/sw/odyssey-apps/ncbi-blast/bin
       BLASTMAT /n/sw/odyssey-apps/ncbi-blast/data
       BLASTDB /n/bluearc/mol/seq/blastdb

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/blat:

      blat module
      ****************************************************

       This module sets up the following environment
       variables for blat:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/blat-34:

      hpc/blat-34
      ****************************************************

       This module sets up the environment for:

       blat version 34
       an alignment tool like BLAST, but structured differently

       Use the command:

       module display hpc/blat-34

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/blitz_gcc-4.1.2:

      hpc/blitz_gcc-4.1.2
      ****************************************************

       This module sets up the environment for:

       Blitz++
       Blitz++ is a C++ class library for scientific computing which provides performance on par with Fortran 77/90. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/blitz_gcc-4.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boinc-7.1.0:

      hpc/boinc-7.1.0
      ****************************************************

       This module sets up the environment for:

       boinc version 7.1.0
       BOINC is an open-source software platform for computing using volunteered resources.

       Use the command:

       module display hpc/boinc-7.1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/28/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.37.0:

      hpc/boost-1.37.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.37.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.37.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.38.0:

      hpc/boost-1.38.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.38.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.38.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.38.0_gcc-4.3.3:

      hpc/boost-1.38.0_gcc-4.3.3
      ****************************************************

       This module sets up the environment for:

       boost version 1.38.0, compiled with gcc 4.3.3
       Boost provides free peer-reviewed portable C++ source libraries

       Use the command:

       module display hpc/boost-1.38.0_gcc-4.3.3

       to see exactly what this module does.

       This module was built by:

       John Brunelle

      ****************************************************

-------------------------------------------------------------------
updated: 11/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.39.0:

      hpc/boost-1.39.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.39.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.39.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.41.0:

      hpc/boost-1.41.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.41.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.41.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.43.0:

      hpc/boost-1.43.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.41.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.43.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.45.0:

      hpc/boost-1.45.0
      ****************************************************

       This module sets up the environment for:

       boost version 1.45.0
       Boost provides free peer-reviewed portable C++ source libraries.

       Use the command:

       module display hpc/boost-1.45.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.46.1:

      hpc/boost-1.46.1
      ****************************************************

       This module sets up the environment for:

       boost C++ library version 1.46.1, GCC 4.1.2
       Boost provides free peer-reviewed portable C++ source libraries. This module was built with GCC 4.1.2 ( Odyssey default ) by Plamen G. Krastev.

       Use the command:

       module display hpc/boost-1.46.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.47.0_python-2.7.1:

      hpc/boost-1.47.0_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       boost C++ library version 1.47.0, GCC 4.1.2, Python 2.7.1
       Boost provides free peer-reviewed portable C++ source libraries. This module was built with GCC 4.1.2 ( Odyssey default ) and Python 2.7.1 by Plamen G. Krastev.

       Use the command:

       module display hpc/boost-1.47.0_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/25/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/boost-1.52.0:

      hpc/boost-1.52.0
      ****************************************************

       This module sets up the environment for:

       boost C++ library version 1.52.0, GCC 4.1.2, Python 2.7.3
       Boost provides free peer-reviewed portable C++ source libraries. This module was built with GCC 4.1.2 ( Odyssey default ) and Python 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display hpc/boost-1.52.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/11/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bpp:

      bpp module
      ****************************************************

       This module sets up the following environment
       variables for bpp:

       Version bpp Version 2.0, October 2009

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bzr-1.5:

      bzr module
      ****************************************************

       This module sets up the following environment
       variables for bzr version 1.5:
       PATH
       MANPATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bzr-2.1.2:

      hpc/bzr-2.1.2
      ****************************************************

       This module sets up the environment for:

       bzr-2.1.2
       Bazaar version control system, version 2.1.2

       Use the command:

       module display hpc/bzr-2.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/05/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/bzr-2.4.2_python-2.7.1:

      hpc/bzr-2.4.2_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       bzr-2.4.2_python-2.7.1
       Bazaar version control system, version 2.4.2 built with Python 2.7.1

       Use the command:

       module display hpc/bzr-2.4.2_python-2.7.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cairo-1.10.2:

      hpc/cairo-1.10.2
      ****************************************************

       This module sets up the environment for:

       cairo version 1.10.2
       a 2D graphics library with support for multiple output devices

       Use the command:

       module display hpc/cairo-1.10.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/08/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cairo-1.8.8:

      hpc/cairo-1.8.8
      ****************************************************

       This module sets up the environment for:

       cairo version 1.8.8
       a 2D graphics library with support for multiple output devices

       Use the command:

       module display hpc/cairo-1.8.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cfitsio-gnu:

      hpc/cfitsio-gnu
      ****************************************************

       This module sets up the environment for:

       CFITSIO Gnu
       C interface to FITS files compiled with GNU compilers

       Use the command:

       module display hpc/cfitsio-gnu

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cfitsio-intel:

      hpc/cfitsio-intel
      ****************************************************

       This module sets up the environment for:

       CFITSIO Intel
       C interface to FITS files compiled with Intel compilers

       Use the command:

       module display hpc/cfitsio-intel

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cfitsio_gcc-4.3.3:

      hpc/cfitsio_gcc-4.3.3
      ****************************************************

       This module sets up the environment for:

       CFITSIO
       C interface to FITS files compiled with GNU version 4.3.3 compilers. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/cfitsio_gcc-4.3.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/charmm_aspuru_lab:

      hpc/charmm_aspuru_lab
      ****************************************************

       This module sets up the environment for:

       CHARMM
       CHARMM is a molecular dynamics simulation and analysis package. This module was built by Plamen G. Krastev.

       Use the command:

       module display hpc/charmm_aspuru_lab

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/charmm_qc_parallel:

      hpc/charmm_qc_parallel
      ****************************************************

       This module sets up the environment for:

       CHARMM
       CHARMM is a molecular dynamics simulation and analysis package. The module has been compiled with Q-chem support. Built by Plamen G. Krastev.

       Use the command:

       module display hpc/charmm_qc_parallel

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/charmm_qc_serial:

      hpc/charmm_qc_serial
      ****************************************************

       This module sets up the environment for:

       CHARMM
       CHARMM is a molecular dynamics simulation and analysis package.The module has been compiled with Q-chem support. Built by Plamen G. Krastev.

       Use the command:

       module display hpc/charmm_qc_serial

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 12/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/chartdirector-5.0.2:

      hpc/chartdirector-5.0.2
      ****************************************************

       This module sets up the environment for:

       ChartDirector, version 5.0.2
       Professional chart component for windows and web applications.

       Use the command:

       module display hpc/chartdirector-5.0.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cloudy-gnu:

      hpc/cloudy-gnu
      ****************************************************

       This module sets up the environment for:

       Cloudy 0.8
       Cloudy 0.8 compile diwth GNU compilers

       Use the command:

       module display hpc/cloudy-gnu

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/clustal-2.0.1:

      Clustal 2.0.1 Module
      ****************************************************

       This module sets up the following environment
       variables:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cmtk-2.2.6:

      hpc/cmtk-2.2.6
      ****************************************************

       This module sets up the environment for:

       CMTK version 2.2.6
       A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. This module has been built by Plamen G Krastev.

       Use the command:

       module display hpc/cmtk-2.2.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/11/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/coreutils-8.21:

      hpc/coreutils-8.21
      ****************************************************

       This module sets up the environment for:

       Coreutils - v8.21
       Coreutils package liunx commands version 8.21 - by Mike Ethier

       Use the command:

       module display hpc/coreutils-8.21

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/28/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cp2k:

      hpc/cp2k
      ****************************************************

       This module sets up the environment for:

       cp2k
       CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems

       Use the command:

       module display hpc/cp2k

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 7/09/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cp2k.gcc_4.6.1:

      hpc/cp2k.gcc_4.6.1
      ****************************************************

       This module sets up the environment for:

       cp2k built with gcc-4.6.1
       CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems

       Use the command:

       module display hpc/cp2k.gcc_4.6.1

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 7/16/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/crystal-1.0.1:

      hpc/crystal-1.0.1
      ****************************************************

       This module sets up the environment for:

       crystal version 1.0.1
       Computational tool for solid state chemistry and physics

       Use the command:

       module display hpc/crystal-1.0.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 1/22/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cubit64_12.0:

      cubit

      ****************************************************

       This module sets up the following environment
       variables for cubit:
       PATH

       Version 12.0

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-2.3:

      hpc/cuda-2.3
      ****************************************************

       This module sets up the environment for:

       CUDA v2.3
       NVidia CUDA driver, toolkit and SDK version 2.3

       Use the command:

       module display hpc/cuda-2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-3.2-Nov2010:

      hpc/cuda-3.2-Nov2010
      ****************************************************

       This module sets up the environment for:

       CUDA v3.2-Nov2010
       NVidia CUDA driver, toolkit and SDK version 3.2-Nov2010

       Use the command:

       module display hpc/cuda-3.2-Nov2010

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-3.2-RC2:

      hpc/cuda-3.2-RC2
      ****************************************************

       This module sets up the environment for:

       CUDA v3.2-RC2
       NVidia CUDA driver, toolkit and SDK version 3.2-RC2

       Use the command:

       module display hpc/cuda-3.2-RC2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-4.0:

      hpc/cuda-4.0
      ****************************************************

       This module sets up the environment for:

       CUDA v4.0
       NVidia CUDA driver, toolkit and SDK version 4.0

       Use the command:

       module display hpc/cuda-4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/26/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-4.2.9:

      hpc/cuda-4.2.9
      ****************************************************

       This module sets up the environment for:

       CUDA v4.2.9
       NVidia CUDA driver, toolkit and SDK version 4.2.9

       Use the command:

       module display hpc/cuda-4.2.9

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/24/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-5.0.35:

      hpc/cuda-5.0.35
      ****************************************************

       This module sets up the environment for:

       CUDA version 5.0.35
       NVidia CUDA driver, toolkit and SDK version 5.0.35. This module has been built by Plamen G Krastev.

       Use the command:

       module display hpc/cuda-5.0.35

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/10/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-driver-2.2:

      hpc/cuda-driver-2.2
      ****************************************************

       This module sets up the environment for:

       CUDA Driver v2.2
       NVidia CUDA driver version 2.2

       Use the command:

       module display hpc/cuda-driver-2.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-driver-2.3:

      hpc/cuda-driver-2.3
      ****************************************************

       This module sets up the environment for:

       CUDA v2.3 driver
       NVidia CUDA driver version 2.3

       Use the command:

       module display hpc/cuda-driver-2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-latest:

      hpc/cuda-latest
      ****************************************************

       This module sets up the environment for:

       CUDA v4.2.9
       NVidia CUDA driver, toolkit and SDK version 4.2.9

       Use the command:

       module display hpc/cuda-latest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/24/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-sdk-2.2:

      hpc/cuda-sdk-2.2
      ****************************************************

       This module sets up the environment for:

       CUDA SDK v2.2
       NVidia CUDA software development kit version 2.2

       Use the command:

       module display hpc/cuda-sdk-2.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-sdk-2.3:

      hpc/cuda-sdk-2.3
      ****************************************************

       This module sets up the environment for:

       CUDA SDK v2.3
       NVidia CUDA software development kit version 2.3

       Use the command:

       module display hpc/cuda-sdk-2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-toolkit-2.2:

      hpc/cuda-toolkit-2.2
      ****************************************************

       This module sets up the environment for:

       CUDA toolkit v2.2
       NVidia CUDA toolkit version 2.2

       Use the command:

       module display hpc/cuda-toolkit-2.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cuda-toolkit-2.3:

      hpc/cuda-toolkit-2.3
      ****************************************************

       This module sets up the environment for:

       CUDA v2.3 toolkit
       NVidia CUDA toolkit version 2.3

       Use the command:

       module display hpc/cuda-toolkit-2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/cython-0.18_python-2.7.3:

      hpc/cython-0.18_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       Cython-0.18, C Extensions for Python
       Cython-0.18, C Extensions for Python. This module was built with Python version 2.7.3 by Plamen G. Krastev.

       Use the command:

       module display hpc/cython-0.18_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Plamen G Krastev

      ****************************************************

-------------------------------------------------------------------
updated: 2/07/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/dateutil-1.5_python-2.7.1:

      hpc/dateutil-1.5_python-2.7.1
      ****************************************************

       This module sets up the environment for:

       dateutil version 1.5
       The dateutil module provides powerful extensions to the standard datetime module, available in Python 2.3+. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/dateutil-1.5_python-2.7.1

       to see exactly what this module does.

       This module was built by:

ERROR: can't read "author": no such variable
updated: 8/23/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/detex:

      hpc/detex
      ****************************************************

       This module sets up the environment for:

       detex
       detex: Remove TeX from a file

       Use the command:

       module display hpc/detex

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/dftd3:

      hpc/dftd3
      ****************************************************

       This module sets up the environment for:

       dftd3
       A dispersion correction for DFT-functionals. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/dftd3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/docutils-0.9.1_python-2.7.3:

      hpc/docutils-0.9.1_python-2.7.3
      ****************************************************

       This module sets up the environment for:

       docutils version 0.9.1, built for python 2.7.3
       Python package for processing plaintext documentation into useful formats, such as HTML, XML, and LaTeX.

       Use the command:

       module display hpc/docutils-0.9.1_python-2.7.3

       to see exactly what this module does.

       This module was built by:

       Mike Ethier

      ****************************************************

-------------------------------------------------------------------
updated: 2/14/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ds9-5.4:

      ds9 module
      ****************************************************

       This module sets up the following environment
       variables for ds9-5.4:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ds9-5.6:

      hpc/ds9-5.6
      ****************************************************

       This module sets up the environment for:

       SAOImage DS9 version 5.6
       Astronomical Data Visualization Application

       Use the command:

       module display hpc/ds9-5.6

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/dysii-1.4.0:

      hpc/dysii-1.4.0
      ****************************************************

       This module sets up the environment for:

       dysii 1.4.0
       dysii is a C++ library for distributed probabilistic inference and learning in large-scale dynamical systems. It features the following:

       Use the command:

       module display hpc/dysii-1.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/eigen-2.0.14:

      hpc/eigen-2.0.14
      ****************************************************

       This module sets up the environment for:

       Eigen version 2.0.14
       Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/eigen-2.0.14

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/emacs-23.2:

      hpc/emacs-23.2
      ****************************************************

       This module sets up the environment for:

       emacs
       emacs editor

       Use the command:

       module display hpc/emacs-23.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/emacs-23.3:

      hpc/emacs-23.3
      ****************************************************

       This module sets up the environment for:

       Emacs, version 23.3
       GNU Emacs is an extensible, customizable text editor—and more.

       Use the command:

       module display hpc/emacs-23.3

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 8/16/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/emboss:

      emboss module
      ****************************************************

       This module sets up the following environment
       variables for emboss:
       PATH /n/sw/emboss/bin
       PLPLOT_LIB /n/sw/emboss/lib
       emboss_acdroot /n/sw/emboss/share/EMBOSS/acd

      ****************************************************

-------------------------------------------------------------------
updated: 11/14/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/enredo-0.5:

      hpc/enredo-0.5
      ****************************************************

       This module sets up the environment for:

       enredo version 0.5
       software to produce colinear segments from extant genomes handling rearrangements

       Use the command:

       module display hpc/enredo-0.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/es-0.97:

      hpc/es-0.97
      ****************************************************

       This module sets up the environment for:

       Elementary Supernova Spectrum Synthesis version 0.97
       SYN++ and SYNAPPS codes: a parallel toolbox for analysis of supernova spectra. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/es-0.97

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/21/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/espresso-4.2.1:

      espresso-4.2.1 Module
      ****************************************************

       This module sets up the following environment
       variables for espresso-4.2.1:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/exonerate-1.4.0:

      hpc/exonerate-1.4.0
      ****************************************************

       This module sets up the environment for:

       exonerate version 1.4.0
       a generic tool for pairwise sequence comparison

       Use the command:

       module display hpc/exonerate-1.4.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/exonerate-2.2.0:

      hpc/exonerate-2.2.0
      ****************************************************

       This module sets up the environment for:

       exonerate version 2.2.0
       a generic tool for pairwise sequence comparison

       Use the command:

       module display hpc/exonerate-2.2.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fastjet-2.4.2:

      hpc/fastjet-2.4.2
      ****************************************************

       This module sets up the environment for:

       FastJet V2.4.2
       The FastJet package provides a fast implementation of the longitudinally invariant kt longitudinally invariant inclusive Cambridge/Aachen and anti-kt jet finders and a uniform interface to external jet finders.

       Use the command:

       module display hpc/fastjet-2.4.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ferret:

      hpc/ferret
      ****************************************************

       This module sets up the environment for:

       FERRET
       an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/ferret

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ffmpeg:

      ffmpeg module
      ****************************************************

       This module sets up the following environment
       variables for ffmpeg :
       PATH
       FPATH
       MANPATH
       CPATH
      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftpack:

      fftpack

      ****************************************************

       This module sets up the following environment
       variables for fftpack:
       LIBRARY_PATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_impi-4.1.0.024_intel-13.0.079:

      hpc/fftw-2.1.5_impi-4.1.0.024_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 13.0.079 and Intel MPI 4.1.0.024 with thread support
       FFTW 2.1.5, compiled with Intel 13.0.079 and Intel MPI 4.1.0.024 with thread support

       Use the command:

       module display hpc/fftw-2.1.5_impi-4.1.0.024_intel-13.0.079

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 10/15/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072:

      hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 11.1.072 and OpenMPI 1.4.2
       FFTW 2.1.5, compiled with Intel 11.1.072 and OpenMPI 1.4.2

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 4/05/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072ib:

      hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072ib
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 11.1.072 and OpenMPI 1.4.2
       FFTW 2.1.5, compiled with Intel 11.1.072 and OpenMPI 1.4.2. This module has been built by Plamen G. Krastev on shock02.

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072ib

       to see exactly what this module does.

       This module was built by:

       pkrastev

      ****************************************************

-------------------------------------------------------------------
updated: 10/24/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072shock:

      hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072shock
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 11.1.072 and OpenMPI 1.4.2
       FFTW 2.1.5, compiled with Intel 11.1.072 and OpenMPI 1.4.2. This module has been built by Plamen G. Krastev on shock02.

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.4.2_intel-11.1.072shock

       to see exactly what this module does.

       This module was built by:

       pkrastev

      ****************************************************

-------------------------------------------------------------------
updated: 10/24/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.4.5_gcc-4.7.0thread:

      hpc/fftw-2.1.5_openmpi-1.4.5_gcc-4.7.0thread
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, GCC 4.7.0 and OpenMPI 1.4.5 with thread support
       FFTW 2.1.5, compiled with GCC 4.7.0 and OpenMPI 1.4.5 with thread support

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.4.5_gcc-4.7.0thread

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 4/20/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.6.2_intel-13.0.079:

      hpc/fftw-2.1.5_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 13.0.079 and OpenMPI 1.6.2 with thread support
       FFTW 2.1.5, compiled with Intel 13.0.079 and OpenMPI 1.6.2 with thread support

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 10/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.6_ics-2012:

      hpc/fftw-2.1.5_openmpi-1.6_ics-2012
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel Cluster Studio 2012 and OpenMPI 1.6 with thread support
       FFTW 2.1.5, compiled with Intel Cluster Studio 2012 and OpenMPI 1.6 with thread support

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.6_ics-2012

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 7/11/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-2.1.5_openmpi-1.6_intel-12.3.174thread:

      hpc/fftw-2.1.5_openmpi-1.6_intel-12.3.174thread
      ****************************************************

       This module sets up the environment for:

       FFTW-2.1.5, Intel 12.3.174 and OpenMPI 1.6 with thread support
       FFTW 2.1.5, compiled with GCC 12.3.174 and OpenMPI 1.6 with thread support

       Use the command:

       module display hpc/fftw-2.1.5_openmpi-1.6_intel-12.3.174thread

       to see exactly what this module does.

       This module was built by:

       pedmon

      ****************************************************

-------------------------------------------------------------------
updated: 5/25/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_openmpi-1.2.5_intel-10.1.015:

      hpc/fftw-3.3.2_openmpi-1.2.5_intel-10.1.015
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.2.5 and Intel 10.1.015

       Use the command:

       module display hpc/fftw-3.3.2_openmpi-1.2.5_intel-10.1.015

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_openmpi-1.6.2_gcc-4.7.2:

      hpc/fftw-3.3.2_openmpi-1.6.2_gcc-4.7.2
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6.2 and GCC 4.7.2

       Use the command:

       module display hpc/fftw-3.3.2_openmpi-1.6.2_gcc-4.7.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_openmpi-1.6.2_intel-13.0.079:

      hpc/fftw-3.3.2_openmpi-1.6.2_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6.2 and Intel 13.0.079 compilers

       Use the command:

       module display hpc/fftw-3.3.2_openmpi-1.6.2_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_openmpi-1.6_gcc-4.7.0:

      hpc/fftw-3.3.2_openmpi-1.6_gcc-4.7.0
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6 and GCC 4.7.0

       Use the command:

       module display hpc/fftw-3.3.2_openmpi-1.6_gcc-4.7.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/09/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_openmpi-1.6_ics-2012:

      hpc/fftw-3.3.2_openmpi-1.6_ics-2012
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6 and Intel Cluster Studio

       Use the command:

       module display hpc/fftw-3.3.2_openmpi-1.6_ics-2012

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 8/03/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw-3.3.2_sandy:

      hpc/fftw-3.3.2_sandy
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with GNU compilers. This module was built by Plamen G. Krastev on sandy.

       Use the command:

       module display hpc/fftw-3.3.2_sandy

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/12/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-mvapich2-gnu:

      fftw2-mvapich2-gnu module
      ****************************************************

       This module sets up the following environment
       variables for fftw2:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-mvapich2-intel:

      fftw2-mvapich2-intel module
      ****************************************************

       This module sets up the following environment
       variables for mvapich2:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-mvapich2-intel-debug:

      fftw2-mvapich2-intel module
      ****************************************************

       This module sets up the following environment
       variables for mvapich2:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-openmpi-gnu:

      fftw2-openmpi-gnu module
      ****************************************************

       This module sets up the following environment
       variables for fftw2:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-openmpi-intel:

      fftw2-openmpi-intel module
      ****************************************************

       This module sets up the following environment
       variables for fftw2:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw2-openmpi-intel-debug:

      fftw2-openmpi-intel module
      ****************************************************

       This module sets up the following environment
       variables for openmpi:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-3.1.2_intel-11.0.083:

      hpc/fftw3-3.1.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.1.2
       FFTW version 3.1.2 compiled with Intel compilers 11.0.083

       Use the command:

       module display hpc/fftw3-3.1.2_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-3.2.1_gnu:

      hpc/fftw3-3.2.1_gnu
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.2.1
       FFTW version 3.2.1 compiled with GNU compilers

       Use the command:

       module display hpc/fftw3-3.2.1_gnu

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-3.2.1_intel-11.0.083:

      hpc/fftw3-3.2.1_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.2.1
       FFTW version 3.2.1 compiled with Intel compilers 11.0.083

       Use the command:

       module display hpc/fftw3-3.2.1_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-mvapich2-intel:

      fftw3-mvapich2-intel module
      ****************************************************

       This module sets up the following environment
       variables for fftw3:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-openmpi-gcc-latest:

      hpc/fftw3-openmpi-gcc-latest
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6.2 and GCC 4.7.2

       Use the command:

       module display hpc/fftw3-openmpi-gcc-latest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/05/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-openmpi-gnu:

      hpc/fftw3-openmpi-gnu
      ****************************************************

       This module sets up the environment for:

       FFTW3.3a2
       FFTW fourier transform vers. 3.3a2 compiled with OpenMPI 1.2.8 and GNU compilers

       Use the command:

       module display hpc/fftw3-openmpi-gnu

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-openmpi-intel:

      hpc/fftw3-openmpi-intel
      ****************************************************

       This module sets up the environment for:

       FFTW3.3a2
       FFTW fourier transform vers. 3.3a2 compiled with OpenMPI 1.2.8 and Intel 10.1.018

       Use the command:

       module display hpc/fftw3-openmpi-intel

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-openmpi-intel-latest:

      hpc/fftw3-openmpi-intel-latest
      ****************************************************

       This module sets up the environment for:

       fftw v. 3.3.2
       FFTW version 3.3.2 compiled with OpenMPI 1.6.2 and Intel 13.0.079 compilers

       Use the command:

       module display hpc/fftw3-openmpi-intel-latest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/02/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fftw3-threaded-intel:

      fftw3-threaded-intel module
      ****************************************************

       This module sets up the following environment
       variables for multi-threaded fftw3:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fiji-1.42e:

      hpc/fiji-1.42e
      ****************************************************

       This module sets up the environment for:

       Fiji 1.42e
       Fiji 1.42e, based on ImageJ 1.42e

       Use the command:

       module display hpc/fiji-1.42e

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/filelight-1.0:

      hpc/filelight-1.0
      ****************************************************

       This module sets up the environment for:

       Filelight version 1.0
       shows your filesystem as a set of concentric pie-charts

       Use the command:

       module display hpc/filelight-1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/firefox-3.6.12:

      hpc/firefox-3.6.12
      ****************************************************

       This module sets up the environment for:

       Firefox, version 3.6.12
       The Firefox web browser, version 3.6.12

       Use the command:

       module display hpc/firefox-3.6.12

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/flens:

      hpc/flens
      ****************************************************

       This module sets up the environment for:

       FLENS
       Flexible Library for Efficient Numerical Solutions is an extremely efficient C++ interface to BLAS and LAPACK. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/flens

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/06/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/flex-2.5.35:

      hpc/flex-2.5.35
      ****************************************************

       This module sets up the environment for:

       flex version 2.5.35
       flex version 2.5.35

       Use the command:

       module display hpc/flex-2.5.35

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/frontier_client--2.7.11--x86_64-slc5-gcc34-opt:

      hpc/frontier_client--2.7.11--x86_64-slc5-gcc34-opt
      ****************************************************

       This module sets up the environment for:

       Frontier 2.7.11 built with gcc 3.4
       provides access to ATLAS Conditions DB

       Use the command:

       module display hpc/frontier_client--2.7.11--x86_64-slc5-gcc34-opt

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/fv:

      fv module
      ****************************************************

       This module sets up the following environment
       variables for fv:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gambit:

      gambit

      ****************************************************

       This module sets up the following environment
       variables for gambit:
       PATH
       LD_LIBRARY_PATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gamess_intell-11.1.072:

      hpc/gamess_intell-11.1.072
      ****************************************************

       This module sets up the environment for:

       gamess
       A program for ab-initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. This module has been built by Plamen G Krastev.

       Use the command:

       module display hpc/gamess_intell-11.1.072

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/21/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/garli-0.96-partMkTest:

      hpc/garli-0.96-partMkTest
      ****************************************************

       This module sets up the environment for:

       GARLI 0.96 parkMkTest
       a special version of GARLI to analyze datasets combining both DNA and protein gene sequences

       Use the command:

       module display hpc/garli-0.96-partMkTest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/garli-0.96-partMkTest_openmpi-1.3.2_intel-11.0.083:

      hpc/garli-0.96-partMkTest_openmpi-1.3.2_intel-11.0.083
      ****************************************************

       This module sets up the environment for:

       GARLI 0.96 parkMkTest
       a special version of GARLI to analyze datasets combining both DNA and protein gene sequences, compiled with OpenMPI support

       Use the command:

       module display hpc/garli-0.96-partMkTest_openmpi-1.3.2_intel-11.0.083

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/garli-0.96b8:

      garli-0.96b8

      ****************************************************

       This module sets up the following environment
       variables for garli version 0.96b8:
       PATH
       LD_LIBRARY_PATH

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-03:

      hpc/gaussian-03
      ****************************************************

       This module sets up the environment for:

       Gaussian 03
       a computational chemistry software program

       Use the command:

       module display hpc/gaussian-03

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-03_ekwan:

      hpc/gaussian-03_ekwan
      ****************************************************

       This module sets up the environment for:

       Gaussian 03
       a computational chemistry software program

       Use the command:

       module display hpc/gaussian-03_ekwan

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-09:

      hpc/gaussian-09
      ****************************************************

       This module sets up the environment for:

       Gaussian 09
       a computational chemistry software program

       Use the command:

       module display hpc/gaussian-09

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-09_D.01:

      hpc/gaussian-09_D.01
      ****************************************************

       This module sets up the environment for:

       Gaussian 09 - version D.01
       a computational chemistry software program. Module built by Mike Ethier

       Use the command:

       module display hpc/gaussian-09_D.01

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/16/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-09_b01:

      hpc/gaussian-09_b01
      ****************************************************

       This module sets up the environment for:

       Gaussian 09
       a computational chemistry software program

       Use the command:

       module display hpc/gaussian-09_b01

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gaussian-09_ekwan:

      hpc/gaussian-09_ekwan
      ****************************************************

       This module sets up the environment for:

       Gaussian 09
       a computational chemistry software program

       Use the command:

       module display hpc/gaussian-09_ekwan

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.1.2:

      hpc/gcc-4.1.2
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.1.2
       GNU compiler version 4.1.2. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/gcc-4.1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.3.3:

      hpc/gcc-4.3.3
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.3.3
       GNU compiler version 4.3.3

       Use the command:

       module display hpc/gcc-4.3.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/25/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.6.1:

      hpc/gcc-4.6.1
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.6.1
       GNU compiler version 4.6.1

       Use the command:

       module display hpc/gcc-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 7/13/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.7.0:

      hpc/gcc-4.7.0
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.7.0
       GNU compiler version 4.7.0

       Use the command:

       module display hpc/gcc-4.7.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/18/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.7.2:

      hpc/gcc-4.7.2
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.7.2
       GNU compiler version 4.7.2

       Use the command:

       module display hpc/gcc-4.7.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-4.8.0:

      hpc/gcc-4.8.0
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.8.0
       GNU compiler version 4.8.0. This module has been built by Plamen G Krastev.

       Use the command:

       module display hpc/gcc-4.8.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/06/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gcc-latest:

      hpc/gcc-latest
      ****************************************************

       This module sets up the environment for:

       GNU Compiler 4.7.2
       GNU compiler version 4.7.2

       Use the command:

       module display hpc/gcc-latest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/26/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gd-intel:

      libgd-intel
      ****************************************************

       This module sets up the following environment
       variables for libgd for intel compiler:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gdal-1.6.1:

      hpc/gdal-1.6.1
      ****************************************************

       This module sets up the environment for:

       GDAL 1.6.1
       GDAL 1.6.1

       Use the command:

       module display hpc/gdal-1.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/genscan-1.0:

      hpc/genscan-1.0
      ****************************************************

       This module sets up the environment for:

       GENSCAN 1.0
       Identification of complete gene structures in genomic DNA

       Use the command:

       module display hpc/genscan-1.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/geos-3.3.8:

      hpc/geos-3.3.8
      ****************************************************

       This module sets up the environment for:

       GEOS version 3.3.8
       GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/geos-3.3.8

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/12/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ghc-6.12.1:

      hpc/ghc-6.12.1
      ****************************************************

       This module sets up the environment for:

       GHC version 6.12.1
       GHC is a state-of-the-art, open source, compiler and interactive environment for the functional language Haskell.

       Use the command:

       module display hpc/ghc-6.12.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/13/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ghc-7.4.1:

      hpc/ghc-7.4.1
      ****************************************************

       This module sets up the environment for:

       GHC version 7.4.1
       GHC is a state-of-the-art, open source, compiler and interactive environment for the functional language Haskell. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/ghc-7.4.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 6/14/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/ghostscript-9.02:

      ghostscript-9.02 module
      ****************************************************

       This module sets up the following environment
       variables for ghostscript-9.02:
       PATH
      ****************************************************

-------------------------------------------------------------------
updated: 5/20/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gifsicle:

      gifsicle

      ****************************************************

       This module sets up the following environment
       variables for gifsicle:
       PATH
       LD_LIBRARY_PATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/git:

      git module
      ****************************************************

       This module sets up the following environment
       variables for git:
       PATH
       LD_LIBRARY_PATH
       MANPATH

       Version 3.1.6

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/git-1.6.4:

      hpc/git-1.6.4
      ****************************************************

       This module sets up the environment for:

       git Version 1.6.4
       git version control system, version 1.6.4

       Use the command:

       module display hpc/git-1.6.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/git-1.7.4:

      hpc/git-1.7.4
      ****************************************************

       This module sets up the environment for:

       git Version 1.7.4
       git version control system, version 1.7.4

       Use the command:

       module display hpc/git-1.7.4

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 3/29/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/glib-2.20.4:

      hpc/glib-2.20.4
      ****************************************************

       This module sets up the environment for:

       glib version 2.20.4
       the core object system used in GNOME

       Use the command:

       module display hpc/glib-2.20.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/glib-2.24.2:

      hpc/glib-2.24.2
      ****************************************************

       This module sets up the environment for:

       glib version 2.24.2
       the core object system used in GNOME

       Use the command:

       module display hpc/glib-2.24.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 9/15/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/globusconnect-1.2:

      hpc/globusconnect-1.2
      ****************************************************

       This module sets up the environment for:

       globusconnect-1.2
       Globus Connect allows you to use Globus Online to transfer files to and from your local machine — even if it is behind a firewall. This module has been built by Plamen G. Krastev

       Use the command:

       module display hpc/globusconnect-1.2

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 2/01/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gmp-5.0.5_intel-13.0.079:

      hpc/gmp-5.0.5_intel-13.0.079
      ****************************************************

       This module sets up the environment for:

       GMP 5.0.5
       GMP 5.0.5 compiled with Intel 13.0.079 compilers

       Use the command:

       module display hpc/gmp-5.0.5_intel-13.0.079

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gmp-5.1.1:

      hpc/gmp-5.1.1
      ****************************************************

       This module sets up the environment for:

       GMP version 5.1.1
       a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. This module has been built with GCC 4.1.2 by Plamen G Krastev.

       Use the command:

       module display hpc/gmp-5.1.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 5/03/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gmp-intel-latest:

      hpc/gmp-intel-latest
      ****************************************************

       This module sets up the environment for:

       GMP 5.0.5
       GMP 5.0.5 compiled with Intel 13.0.079 compilers

       Use the command:

       module display hpc/gmp-intel-latest

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 10/12/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gmsh-2.5.0:

      hpc/gmsh-2.5.0
      ****************************************************

       This module sets up the environment for:

       Gmsh, Version 2.5.0
       A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

       Use the command:

       module display hpc/gmsh-2.5.0

       to see exactly what this module does.

       This module was built by:

       cwalker

      ****************************************************

-------------------------------------------------------------------
updated: 4/01/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gnuplot-4.2.3:

      hpc/gnuplot-4.2.3
      ****************************************************

       This module sets up the environment for:

       Gnuplot version 4.2.3
       Gnuplot: Plotting program from GNU. Version 4.2.3

       Use the command:

       module display hpc/gnuplot-4.2.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gnuplot-4.2.5:

      hpc/gnuplot-4.2.5
      ****************************************************

       This module sets up the environment for:

       Gnuplot version 4.2.5
       Gnuplot: Plotting program from GNU. Version 4.2.5

       Use the command:

       module display hpc/gnuplot-4.2.5

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/grads-2.0.a5:

      grads

      ****************************************************

       This module sets up the following environment
       variables for grads:
       PATH GADDIR

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gromacs-4.0.4:

      hpc/gromacs-4.0.4
      ****************************************************

       This module sets up the environment for:

       GROMACS version 4.0.4
       fast, free, and flexible molecular dynamics

       Use the command:

       module display hpc/gromacs-4.0.4

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gromacs-4.5.3:

      hpc/gromacs-4.5.3
      ****************************************************

       This module sets up the environment for:

       GROMACS version 4.5.3
       fast, free, and flexible molecular dynamics

       Use the command:

       module display hpc/gromacs-4.5.3

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/17/2011

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gromacs-4.6.1:

      hpc/gromacs-4.6.1
      ****************************************************

       This module sets up the environment for:

       GROMACS version 4.6.1
       fast, free, and flexible molecular dynamics. This module has been built by Plamen G. Krastev.

       Use the command:

       module display hpc/gromacs-4.6.1

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 3/08/2013

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gsl-1.15_gcc-4.7.0:

      hpc/gsl-1.15_gcc-4.7.0
      ****************************************************

       This module sets up the environment for:

       GNU Science Library 1.15
       GNU Science Library 1.15 compiled with GNU 4.7.0 compilers

       Use the command:

       module display hpc/gsl-1.15_gcc-4.7.0

       to see exactly what this module does.

      ****************************************************

-------------------------------------------------------------------
updated: 4/19/2012

-------------------------------------------------------------------
Module Specific Help for /n/sw/odyssey-apps/modules-3.2.6/Modules/modulefiles/hpc/gsl-1.15_gcc-4.7.2:

      hpc/gsl-1.15_gcc-4.7.2
      ****************************************************

       This module sets up the environment for:

       GNU Science Library 1.15
  &