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 nonsynonymous (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. Availability: ADAPTSITE is available free of charge at the World-Wide Web sites http://mep.bio.psu.edu/adaptivevol.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 * To whom correspondence should be addressed.