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Bioinformatics Advance Access originally published online on June 17, 2009
Bioinformatics 2009 25(17):2286-2288; doi:10.1093/bioinformatics/btp368
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Nicolas Lartillot 1,*, Thomas Lepage 1 and Samuel Blanquart 2

1 Département de Biochimie, Université de Montréal, Montréal, Québec, Canada and 2 Département d'Informatique, LIRMM, Montpellier, France

* To whom correspondence should be addressed.


  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: nicolas.lartillot{at}umontreal.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on January 26, 2009; revised on June 9, 2009; accepted on June 10, 2009

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