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. Availability: ADAPTSITE is available free of charge at the World-Wide Web sites http://mep.bio.psu.edu/adaptiveol.html and http://www.cib.nig.ac.jp/dda/yossuzuk/welcome. html. The package includes the source code written in C, binary files for UNIX operating systems, manual, and example files. Contact: yis1@psu.edu
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