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PhyloBayes

Description

phylobayes website

PhyloBayes (Lartillot et al, 2009) 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 (Lartillot and Philippe, 2004). 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.

Environment Modules

Run module spider phylobayes to find out what environment modules are available for this application.

Environment Variables

  • HPC_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., & Philippe, H. (2004). A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution, 21(6), 1095-1109. https://doi.org/10.1093/molbev/msh112
  • Lartillot, N., & Philippe, H. (2006). Computing Bayes factors using thermodynamic integration. Systematic Biology, 55(2), 195-207. https://doi.org/10.1080/10635150500433722
  • Lartillot, N., Brinkmann, H., & Philippe, H. (2007). Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology, 7(Suppl 1), S4. https://doi.org/10.1186/1471-2148-7-S1-S4

Categories

biology, phylogenetics