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.
Bibliographical noteFunding 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.
ASJC Scopus subject areas
- Statistics and Probability
- Molecular Biology
- Computer Science Applications
- Computational Theory and Mathematics
- Computational Mathematics