K-Pax contains an implementation of a Bayesian model-based method for simultaneously classifying aligned proteins into functionally divergent subgroups and identifying their function specific residues
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Marttinen, P., Corander, J., Törönen, P. and Holm, L. (2006).
Bayesian search of functionally divergent protein subgroups and their function specific residues.
Bioinformatics, 22, 2466-2474.