Prottest
From Vd
Contents |
ProtTest
General information
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, mtREV, Dayhoff, 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.
Input
An alignment in Nexus format.
Quick start
Choose your aligned Nexus file, give the job a name and choose ProtTest from the applications list. On the next page you can choose the statistical model of selection (AiC, BiC, AiCc and LnL), for most purposes the default AiC is more than sufficient. You also have the option to deselect models of evolution if you already know the most likely model (this option will of course save processing time).
Output
The results are printed to a “.out” file, which can be simply opened in a text editing program.
You can now use the optimal evolutionary model obtained from ProtTest as input for a phylogenetic inference.
Homepage
http://darwin.uvigo.es/software/prottest.html
Author contact information
Federico Abascal: fabascal@cnb.uam.es
Rafael Zardoya: rafaz@mncn.csic.es
David Posada: dposada@uvigo.es
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]