Improving Phylogenetic Inference with a Semiempirical Amino Acid Substitution Model
نویسندگان
چکیده
منابع مشابه
A metric model of amino acid substitution
MOTIVATION We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed and sensitivity among competing computational methods of determining sequence homology. A metric model of evolution is a prerequisite for the development of an entire class of fast sequence analysis...
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GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2012
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/mss229