PhyloBayes

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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.

Availability

Program is available in several versions. Usable modules:

phylobayes-3.3b
phylobayes-mpi-1.5a
phylobayes-mpi-1.7

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 How to compute/Parallelization.

Documentation

Documentation is available on WWW server.

Licence

GPL

Program administrator

meta@cesnet.cz

Homepage

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