Difference between revisions of "PhyloBayes"
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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. | 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. | ||
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Revision as of 02:41, 10 August 2012
Description
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.
Execution Environment and 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