jModelTest is a new program designed for the statistical selection of models of nucleotide substitution, based on the "Phyml" algorithm. It offers five selection strategies, including hierarchical and dynamic likelihood ratio tests, the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC), and a decision-theoretic performance-based approach. The program 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 on Mac OSX, Windows, and Unix systems. It includes a front-end computational pipeline that integrates other programs for tasks such as sequence alignment, likelihood calculations, and tree consensus. The program provides flexibility in defining candidate models and supports various information criteria for model selection. It also offers methods to handle model selection uncertainty and compute model-averaged phylogenies. jModelTest is freely available for academic use from the software section at http://darwin.uvigo.es.jModelTest is a new program designed for the statistical selection of models of nucleotide substitution, based on the "Phyml" algorithm. It offers five selection strategies, including hierarchical and dynamic likelihood ratio tests, the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC), and a decision-theoretic performance-based approach. The program 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 on Mac OSX, Windows, and Unix systems. It includes a front-end computational pipeline that integrates other programs for tasks such as sequence alignment, likelihood calculations, and tree consensus. The program provides flexibility in defining candidate models and supports various information criteria for model selection. It also offers methods to handle model selection uncertainty and compute model-averaged phylogenies. jModelTest is freely available for academic use from the software section at http://darwin.uvigo.es.