PROTTEST is a free and open source program for selecting the model of protein evolution that best fits a given set of sequences (alignment).
PROTTEST 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 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.
Requirements:
· Java
