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MBE Advance Access originally published online on April 8, 2008
Molecular Biology and Evolution 2008 25(7):1253-1256; doi:10.1093/molbev/msn083
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Letters

jModelTest: Phylogenetic Model Averaging

David Posada

Departamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain

E-mail: dposada{at}uvigo.es.

Accepted for publication April 2, 2008.

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.

Key Words: model selection • likelihood ratio tests • AIC • BIC • performance-based selection • statistical phylogenetics

Sudhir Kumar, Associate Editor


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