Bioinformatics for DNA Sequence Analysis

Volume 537 of the series Methods in Molecular Biology pp 93-112


Selection of Models of DNA Evolution with jModelTest

  • David PosadaAffiliated withDepartamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de Vigo

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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.

Key words

Model selection likelihood ratio tests AIC BIC performance-based selection statistical phylogenetics