Bioinformatics Vol. 17 no. 7 2001
Pages 660-661
© 2001 Oxford University Press
Applications Note |
ADAPTSITE: detecting natural selection at single amino acid sites
1 Institute of Molecular Evolutionary
Genetics and Department of Biology, Pennsylvania State University,
328 Mueller Laboratory, University Park, PA 16802, USA
2 Center for Information Biology, National
Institute of Genetics, 1111 Yata, Mishima-shi, Shizuoka-ken
411-8540, Japan
Received on January 15, 2001
; revised on March 9, 2001
; accepted on March 15, 2001
Summary: 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{at}psu.edu
* To whom correspondence should be addressed.
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