ADAPTSITE: detecting natural selection at single amino acid sites | Zendy

Yoshiyuki Suzuki | Zendy; Takashi Gojobori | Zendy; Masatoshi Nei | Zendy

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ADAPTSITE: detecting natural selection at single amino acid sites

Author(s) -

Yoshiyuki Suzuki,

Takashi Gojobori,

Masatoshi Nei

Publication year - 2001

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/17.7.660

Subject(s) - nonsynonymous substitution , phylogenetic tree , computer science , source code , natural selection , r package , biology , tree (set theory) , selection (genetic algorithm) , genetics , combinatorics , computational biology , theoretical computer science , mathematics , programming language , artificial intelligence , gene , genome

ADAPTSITE is a program package for detecting natural selection at single amino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program infers ancestral codons at all interior nodes, and computes the total numbers of synonymous (c(S)) and nonsynonymous (c(N)) substitutions as well as the average numbers of synonymous (s(S)) and nonsynonymous (s(N)) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by s(S) / (s(S) + s(N)) and s(N) / (s(S) + s(N)), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining c(S) and c(N).

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