Spidermonkey: Rapid detection of co-evolving sites using Bayesian graphical models

Bioinformatics

Volumn 24, Issue 17, 2008, Pages 1949-1950

  Poon, Art F Y ^a   Lewis, Fraser I ^b   Frost, Simon D W ^a   Kosakovsky Pond, Sergei L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCOTTISH AGRICULTURAL COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BAYESIAN LEARNING; INFORMATION PROCESSING; MACHINE LEARNING; MAXIMUM LIKELIHOOD METHOD; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE DATABASE;

EID: 50549084385     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn313     Document Type: Article

References (11)

1. Felsenstein,J. (1985) Phylogenies and the comparative method. Am. Nat., 125, 1-15.
2. Friedman,N. and Koller,D. (2003) Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks. Mach. Learn., 50, 95-125.
3. Gansner,E. and North,S. (2000) An open graph visualization system and its applications to software engineering. In Software: Practice and Experience. John Wiley & Sons, Ltd., Chichester, New York.
4. Kosakovsky Pond,S.L. and Frost,S.D.W. (2005a) Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 21, 2531-2533.
5. Kosakovsky Pond,S.L. and Frost,S.D.W. (2005b) A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol., 22, 478-485.
6. Kosakovsky Pond,S.L. and Frost,S.D.W. (2005c) Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol., 22, 1208-1222.
7. Kosakovsky Pond,S.L. et al. (2005) HyPhy: Hypothesis testing using phylogenies. Bioinformatics, 21, 676-679.
8. Pearl,J. (1988) Probabilistic reasoning in intelligent systems: networks of plausible inference. Morgan Kaufmann Publishers, San Mateo, CA, pp. 552.
9. Poon,A.F.Y. et al. (2007) An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput. Biol., 3, e231.
10. Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
11. Scheffler,K. et al. (2006) Robust inference of positive selection from recombining coding sequences. Bioinformatics, 22, 2493-2499.