Codep is a novel method for the determination of interacting protein partners by maximizing co-evolutionary signals. The order of sequences in the multiple sequence alignments from two protein families is determined in such a manner as to maximize the similarity of substitution patterns at amino acid sites in the two alignments and, thus, phylogenetic congruency.
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Codep: maximizing co-evolutionary interdependencies to discover interacting proteins.
Tillier, E. R. M., L. Biro, G. Li and D. Tillo,
PROTEINS: Structure, Function and Bioinformatics (2006) 63: 822-31