PhyloBayes

Description

phylobayes website  

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.

Required Modules

modules documentation

Serial

• phylobayes

Parallel (MPI)

• intel/2012
• openmpi/1.6
• phylobayes/1.4f

System Variables

• HPC_{{#uppercase:phylobayes}}_DIR - installation directory
• HPC_PHYLOBAYES_BIN - executable directory
• HPC_PHYLOBAYES_DOC - documentation directory

Citation

If you publish research that uses phylobayes you have to cite it as follows:

Lartillot N, Phillipe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21: 1095–1109.

Lartillot N, Philippe H (2006) Computing Bayes factors using thermodynamic integration. Syst Biol 55: 195–207.

Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 2007;7(Suppl 1):S4. doi: 10.1186/1471-2148-7-S1-S4.