Journal Article

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

Nicolas Lartillot, Thomas Lepage and Samuel Blanquart

in Bioinformatics

Volume 25, issue 17, pages 2286-2288
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp368
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

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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@umontreal.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1924 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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