ADAPTSITE: detecting natural selection at single amino acid sites

ADAPTSITE is a program package for detecting natural selection at single am ino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program infers ancestral codons at all inter ior nodes, and computes the total numbers of synonymous (c(S)) and nonsynon ymous (c(N)) substitutions as well as the average numbers of synonymous (s( S)) and nonsynonymous (s(N)) sites for each colon site. The probabilities o f 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 hypothesi s of selective neutrality is tested for each codon site, assuming a binomia l distribution for the probability of obtaining c(S) and c(N).