jModelTest: Phylogenetic Model Averaging | Zendy

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jModelTest: Phylogenetic Model Averaging

Author(s) -

David Posada

Publication year - 2008

Publication title -

molecular biology and evolution

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 6.637

H-Index - 218

eISSN - 1537-1719

pISSN - 0737-4038

DOI - 10.1093/molbev/msn083

Subject(s) - akaike information criterion , bayesian information criterion , biology , java , model selection , substitution (logic) , phylogenetic tree , unix , software , darwin (adl) , maximum likelihood , bayesian probability , selection (genetic algorithm) , computer science , bayes factor , bayes' theorem , statistics , machine learning , artificial intelligence , programming language , mathematics , genetics , software engineering , gene

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

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