Introduction

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

ProtTest is written in Java and uses the program PhyML (Guindon and Gascuel, 2003) for the maximum likelihood (ML) estimation of phylogenetic trees and model parameters. The current version of ProtTest (3.2) includes 15 different rate matrices that result in 120 different models when we consider rate variation among sites (+I: invariable sites; +G: gamma-distributed rates) and the observed amino acid frequencies (+F).

Usage

 module load bioinformatics/prottest

Installation

cd /sw/bioinformatics/prottest/3.2.20120316/src
tar -zxvf prottest-3.2-20120316.tar.gz
mv * ../../
cd /sw/bioinformatics/prottest/3.2.20120316

Reference

1. http://code.google.com/p/prottest3/