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Molecular Biology and Evolution 18:1435-1441 (2001)
© 2001 Society for Molecular Biology and Evolution

Secator: A Program for Inferring Protein Subfamilies from Phylogenetic Trees

Nicolas Wicker, Guy René Perrin, Jean Claude Thierry and Olivier Poch

LSIIT-ICPS (AXE E), UPRES-A CNRS 70005 Université Louis Pasteur, Illkirch, France
Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, Illkirch, France

With the huge increase of protein data, an important problem is to estimate, within a large protein family, the number of sensible subsets for subsequent in-depth structural, functional, and evolutionary analyses. To tackle this problem, we developed a new program, Secator, which implements the principle 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 values. The quality of the clusters obtained by Secator is verified by a separate Jackknife study. The method is demonstrated on 24 large protein families covering a wide spectrum of structural and sequence conservation and its usefulness and accuracy with real biological data is illustrated on two well-studied protein families (the Sm proteins and the nuclear receptors).


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