Secator: A program for inferring protein subfamilies from phylogenetic trees

With the huge increase of protein data, an important problem is to estimate , within a large protein family, the number of sensible subsets for subsequ ent in-depth structural, functional, and evolutionary analyses. To tackle t his problem, we developed a new program, Secator, which implements the prin ciple of an ascending hierarchical method using a distance matrix based on a multiple alignment of protein sequences. Dissimilarity values assigned to the nodes of a deduced phylogenetic tree are partitioned by a new stopping rule introduced to automatically determine the significant dissimilarity v alues. The quality of the clusters obtained by Secator is verified by a sep arate Jackknife study. The method is demonstrated on 24 large protein famil ies covering a wide spectrum of structural and sequence conservation and it s usefulness and accuracy with real biological data is illustrated on two w ell-studied protein families (the Sm proteins and the nuclear receptors).