PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

TLDR

Probabilistic models for DNA and protein evolution have been proposed for phylogenetic reconstruction and molecular dating, yet no common implementation exists to combine these features and assess their joint improvement of accuracy. The authors present PhyloBayes 3 to perform Bayesian phylogenetic reconstruction and molecular dating. PhyloBayes 3 supports a wide array of amino acid and nucleotide substitution models, including empirical mixtures, non‑parametric models, and alternative clock relaxation processes. PhyloBayes 3 is freely available at http://www.phylobayes.org. The software runs on Linux, macOS, and Windows, can be contacted at [e-mail], and has supplementary data available online.

Abstract

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. Availability: PhyloBayes is freely available from our web site http://www.phylobayes.org. It works under Linux, Mac OsX and Windows operating systems. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.