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PROTTEST: Selection of best-fit models of protein evolution

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© 2004-20011 Federico Abascal, Rafael Zardoya and David Posada

Current version is 2.4 (October 09).

Use of ProtTest's logo kindly allowed by IconBAZAAR.




Check the new High Performace Computing version of Prottest: PROTTEST 3

PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). This java program is based on the Phyml program (for maximum likelihood calculations and optimization of parameters) and uses the PAL library as well. Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand.

Operative systems
ProtTest runs on Mac OSX (PPC / Intel), Windows and Linux.

Citation
Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics: 21(9):2104-2105.

In addition, given that ProtTest uses intensively Phyml and PAL, we encourage users to cite these programs as well when using ProtTest:
- Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704. [Phyml]
- Drummond, A., and K. Strimmer. 2001. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663. [PAL]

ProtTest registration form

Before downloading this program, we ask users to register. This allows us 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.

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This document last modified Saturday May 28, 2011