Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments

Bioinformatics

Volumn 21, Issue 10, 2005, Pages 2531-2533

  Kosakovsky Pond, Sergei L ^a   Frost, Simon D W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; CODON; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; DATAMONKEY; GENETIC VARIABILITY; INFORMATION PROCESSING; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 17744395033     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti320     Document Type: Article

References (11)

1. Altschul,S. et al. (1997) Gapped BLAST and PSI-BLAST: anew generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Kosakovsky Pond,S.L. and Frost,S.D. (2005a) A simple hierarchical approach to modeling distributions of substitution rates. Mol. Biol. Evol., 22, 223-234.
3. Kosakovsky Pond,S.L. and Frost,S.D. (2005b) Not so different after all: a comparison of methods for detecting amino-acid sites under selection. Mol. Biol. Evol., Advance Access published February 9, 2005, doi:10.1093/molbev/msi 105.
4. Kosakovsky Pond,S.L. and Muse,S.V. (2005) Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol., in revision.
5. Kosakovsky Pond,S.L. et al. (2004) HyPhy: hypothesis testing using phylogenies. Bioinformatics, 21, 676-679.
6. Nielsen,R. and Yang,Z.H. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929-936.
7. Saitou,N. and Nei,M. (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
8. Suzuki,Y. and Gojobori,T. (1999) A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol., 16, 1315-1328.
9. Suzuki,Y. et al. (2001) ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics, 17, 660-661.
10. Yang,Z. (2002) Inference of selection from multiple species alignments. Curr. Opin. Genet. Develop., 12, 688-694.
11. Yang,Z.H. (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci., 13, 555-556.