PhyloBayes 3: A Bayesian Software Package for Phylogenetic Reconstruction and Molecular Dating

Bioinformatics. 2009 Sep 1;25(17):2286-8. doi: 10.1093/bioinformatics/btp368. Epub 2009 Jun 17.

Abstract

Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy.

Results: We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bayes Theorem*
  • Computational Biology / methods*
  • Databases, Nucleic Acid
  • Phylogeny*
  • Predictive Value of Tests
  • Reproducibility of Results
  • Software*
  • Time Factors