PhyloBayes

Description

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PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is a mixture model especially devised to account for site-specific features of protein evolution. It is particularly well suited for large multigene alignments, such as those used in phylogenomics. Template:App Location

Available versions

• 3.3b

Running the application using modules

To use phylobayes with the environment modules system at HPC the following commands are available:

Get module information for phylobayes:

$module spider phylobayes

Load the default application module:

$module load phylobayes

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_PHYLOBAYES_DIR - directory where phylobayes is located.
• HPC_PHYLOBAYES_BIN - executable directory
• HPC_PHYLOBAYES_DOC - documentation directory