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.
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.
Authors: Stephen A Smith; Nerida G Wilson; Freya E Goetz; Caitlin Feehery; Sónia C S Andrade; Greg W Rouse; Gonzalo Giribet; Casey W Dunn Journal: Nature Date: 2011-10-26 Impact factor: 49.962
Authors: Davide Pisani; Walker Pett; Martin Dohrmann; Roberto Feuda; Omar Rota-Stabelli; Hervé Philippe; Nicolas Lartillot; Gert Wörheide Journal: Proc Natl Acad Sci U S A Date: 2015-11-30 Impact factor: 11.205
Authors: Justin C Havird; Kevin M Kocot; Pamela M Brannock; Johanna T Cannon; Damien S Waits; David A Weese; Scott R Santos; Kenneth M Halanych Journal: J Mol Evol Date: 2015-03-11 Impact factor: 2.395