jModelTest: Phylogenetic Model Averaging

by: David Posada

Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1253-1256.

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DOI, HighWire, Pubmed, Hubmed, DOI, http://dx.doi.org/10.1093/molbev/msn083

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Abstract

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 "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. 10.1093/molbev/msn083

@article{posada08, abstract = {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 "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. 10.1093/molbev/msn083}, author = {Posada, David }, citeulike-article-id = {2932122}, doi = {http://dx.doi.org/10.1093/molbev/msn083}, journal = {Mol Biol Evol}, keywords = {methods, model\_choice, tools}, month = {July}, number = {7}, pages = {1253--1256}, posted-at = {2008-06-26 21:29:49}, priority = {2}, title = {jModelTest: Phylogenetic Model Averaging}, url = {http://dx.doi.org/10.1093/molbev/msn083}, volume = {25}, year = {2008} }

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TY - JOUR ID - posada08 L3 - citeulike-article-id:2932122 N2 - 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 "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. 10.1093/molbev/msn083 IS - 7 JF - Mol Biol Evol EP - 1256 TI - jModelTest: Phylogenetic Model Averaging VL - 25 SP - 1253 KW - methods KW - model_choice KW - tools AU - Posada, David PY - 2008/July/01/ UR - http://dx.doi.org/10.1093/molbev/msn083 ER -

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