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jMODELTEST: phylogenetic model averaging

© 2008-onwards David Posada

Current version is 0.1.1

jMODELTEST ijModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies. Please note that the DT weights are very gross

Operative systems
Although jModelTest it is optimized for MacOS X Intel, executables are provided to run the program under MacOS X PPC, Windows XP and Linux. In order to avoid potential problems during execution, the program folder and folders therein should be located under a path without spaces, although this is not always necessary.

Citation
Posada D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256.

In addition, given that jModelTest uses intensively Phyml, we ask users to cite this program as well when using jModelTest:

Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.

For additional background see also: Posada D and Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808

jModeltest registration form

Before download this program, I ask users to register. This allows me to inform about bugs and updates in a more efficient way. Indeed, users will be able to unregister at any time, and email addresses will not be used for any purpose other than to inform about this program.

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Disclaimer: These programs are free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. These programs are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Correspondence about this program should be addressed to David Posada at



This document last modified Saturday May 28, 2011