LETTERS jModelTest: Phylogenetic Model Averaging

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 ‘‘decisiontheoretic 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.