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

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

Author information

1
Département de Biochimie, Université de Montréal, Montréal, Québec, Canada. nicolas.lartillot@umontreal.ca

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.

PMID:
19535536
DOI:
10.1093/bioinformatics/btp368
[Indexed for MEDLINE]
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