Selection of Models of DNA Evolution with jModelTest

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Abstract

jModelTest is a bioinformatic tool for choosing among different models of nucleotide substitution. The program implements five different model selection strategies, including hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a performance-based decision theory method (DT). The output includes estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates, including model-averaged phylogenies. jModelTest is a Java program that runs under Mac OSX, Windows, and Unix systems with a Java Run Environment installed, and it can be freely downloaded from http://darwin.uvigo.es.