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Molecular Biology and Evolution 18:1502-1511 (2001)
© 2001 Society for Molecular Biology and Evolution

Phylogenetic Analyses of Amino Acid Variation in the Serpin Proteins

William R. Atchley, Tatiana Lokot, Kurt Wollenberg, Andreas Dress and Hermann Ragg

Department of Genetics, North Carolina State University
Faculty of Mathematics
Faculty of Technology, University of Bielefeld, Bielefeld, Germany

Phylogenetic analyses of 110 serpin protein sequences revealed clades consistent with independent phylogenetic analyses based on exon-intron structure and diagnostic amino acid sites. Trees were estimated by maximum likelihood, neighbor joining, and partial split decomposition using both the BLOSUM 62 and Jones-Taylor-Thornton substitution matrices. Neighbor-joining trees gave results closest to those based on independent analyses using genomic and chromosomal data. The maximum-likelihood trees derived using the quartet puzzling algorithm were very conservative, producing many small clades that separated groups of proteins that other results suggest were related. Independent analyses based on exon-intron structure suggested that a neighbor-joining tree was more accurate than maximum-likelihood trees obtained using the quartet puzzling algorithm.


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