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).

http://darwin.uvigo.es/software/prottest.html

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