BayesPhylogenies

BayesPhylogenies is a general package for inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. See http://www.evolution.reading.ac.uk/BayesTrees.html for more information.

---

Software Modules

bio/BayesPhylogenies-1.1

This is the standard binary downloaded from the project’s home page. (Note that the probram misidentifies itself as version 1.0; it really is 1.1.)

bio/BayesPhylogenies-1.1_openmpi-1.3.2_intel-11.0.083

This is version built to run in parallel across many nodes. See the LSF: Running MPI Jobs on Odyssey page in the FAQ for running openmpi jobs on Odyssey. In order to determine what to use for bsub‘s -n , the most relevant BayesPhylogenies parameter appears to be chains.

bio/BayesPhylogenies-1.1_openmp

This is a version built with threading support, mainly for testing. The MPI version scales much better, as the threaded version can only use the cores on one node. However, Andrew Meade reports that the MPI and openMP versions work on different parts of the code, so we’re still experimenting with combining them.

---

Older Software Modules

hpc/BayesPhylogenies

This is version 1.0.