PhyloBayes

Description

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments.

License

GPL

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of phylobayes and load default version of phylobayes as

module avail phylobayes/ # list available modules
module load phylobayes   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail phylobayes

and choose explicit version you want to use.

Normal version

Initialize environment with command module add. Example:

module add phylobayes-3.3b

and run command pb.

Parallel version

Initialize environment with command module add. Example:

module add phylobayes-mpi-1.5a

and run pb_mpi. The version numbers differs in parallel application, so version 1.5a is the last in May 2014.

Notice: This application supports parallel computing (MPI, OpenMP) which can have weird consequences. For more details about parallel computing visit the page Parallelization.

Documentation

Documentation is available on WWW server.

Homepage

URL: http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm