ADAPTSITE: Detecting natural selection at single amino acid sites

Yoshiyuki Suzuki; Takashi Gojobori; Masatoshi Nei

doi:10.1093/bioinformatics/17.7.660

ADAPTSITE: Detecting natural selection at single amino acid sites

Yoshiyuki Suzuki^*, Takashi Gojobori, Masatoshi Nei

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

67 Scopus citations

Abstract

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 non-synonymous (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.

Original language	English (US)
Pages (from-to)	660-661
Number of pages	2
Journal	Bioinformatics
Volume	17
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/17.7.660
State	Published - 2001
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/17.7.660

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title = "ADAPTSITE: Detecting natural selection at single amino acid sites",

abstract = "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 (cS) and nonsynonymous (cN) substitutions as well as the average numbers of synonymous (sS) and non-synonymous (sN) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by sS/(sS + sN) and sN/(sS + sN), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining cS and cN.",

author = "Yoshiyuki Suzuki and Takashi Gojobori and Masatoshi Nei",

note = "Funding Information: The authors thank two anonymous reviewers for providing valuable comments. This work was partially supported by a research grant from the National Institutes of Health to M.N. Y.S. is supported by the JSPS Research Fellowships for Young Scientists.",

year = "2001",

doi = "10.1093/bioinformatics/17.7.660",

language = "English (US)",

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journal = "Bioinformatics",

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T2 - Detecting natural selection at single amino acid sites

AU - Suzuki, Yoshiyuki

AU - Gojobori, Takashi

AU - Nei, Masatoshi

N1 - Funding Information: The authors thank two anonymous reviewers for providing valuable comments. This work was partially supported by a research grant from the National Institutes of Health to M.N. Y.S. is supported by the JSPS Research Fellowships for Young Scientists.

PY - 2001

Y1 - 2001

N2 - 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 (cS) and nonsynonymous (cN) substitutions as well as the average numbers of synonymous (sS) and non-synonymous (sN) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by sS/(sS + sN) and sN/(sS + sN), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining cS and cN.

AB - 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 (cS) and nonsynonymous (cN) substitutions as well as the average numbers of synonymous (sS) and non-synonymous (sN) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by sS/(sS + sN) and sN/(sS + sN), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining cS and cN.

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ADAPTSITE: Detecting natural selection at single amino acid sites

Abstract

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