ProtTest 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.

ProtTest is a bioinformatic tool for the selection of the most appropriate model of protein evolution (among the set of candidate models) for the data at hand. ProtTest makes this selection by finding the model with the smallest Akaike Information Criterion
(AIC) or Bayesian Information Criterion (BIC) score. At the same time, ProtTest obtains model-averaged estimates of different parameters (Posada and Buckley 2004) and calculates the importance of each of these parameters. ProtTest differs from its
nucleotide homolog Modeltest (Posada and Crandall 1998) in that it does not include likelihood ratio tests (many models implemented in ProtTest are not nested).

How to use:
1. Input an alignment in phylip (recommended) or nexus-sequential format.
2. Optionally you can input a tree topology in newick format; if not, a BIONJ tree will be calculated.
3. Select the strategy: fast (fixed tree; optimization of model parameters and branch lengths; this is the strategy used by Modeltest) or slow (optimization of model, branches and topology of the tree) (see the "Optimization strategies" section below).
4. Optionally, you might want to restrict the set of candidate models. For that you should click the "models" button. Read first the section "Restricting the set of candidate models".
5. And click the "Start" button!

The license of this software is Free, you can free download and free use this cad software.