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MBE Advance Access published online on April 8, 2008
Molecular Biology and Evolution, 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

Letter

jModelTest: Phylogenetic Model Averaging

David Posada

Departamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de, Vigo, 36310 Vigo, Spain

Contact address: David Posada, Edificio de Ciencias Experimentales, Campus Universitario, 36310 Vigo, Spain, E-mail: dposada{at}uvigo.es, Tel.: +34 986 812038, Fax: +34 986 812556

Received for publication February 4, 2008. Revision received April 1, 2008. 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). It implements five 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


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