Detecting signatures of selection from DNA sequences using Datamonkey.
Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest of the population, or increases its genetic diversity, and negative selection removes those alleles that are deleterious. Codon-based models of molecular evolution are able to infer signatures of selection from alignments of homologous sequences by estimating the relative rates of synonymous (dS) and non-synonymous substitutions (dN). Datamonkey (http://www.datamonkey.org) provides a user-friendly web interface to a wide collection of state-of-the-art statistical techniques for estimating dS and dN and identifying codons and lineages under selection, even in the presence of recombinant sequences.
Poon
Art F Y
AF
Antiviral Research Center, Department of Pathology, University of California San Diego, La Jolla, CA, USA.
Frost
Simon D W
SD
Pond
Sergei L Kosakovsky
SL
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D014644:Genetic Variation; D020407:Internet; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface