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Detecting Signatures of Selection from DNA Sequences Using Datamonkey

  • Art F.Y. Poon
  • Simon D.W. Frost
  • Sergei L. Kosakovsky Pond
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 537)

Abstract

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.

Key words

Positive selection adaptive evolution dN and dS estimation HyPhy phylogenetic analysis maximum likelihood inference parallel algorithms web service 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Art F.Y. Poon
    • 1
  • Simon D.W. Frost
    • 1
  • Sergei L. Kosakovsky Pond
    • 1
  1. 1.Antiviral Research Center, Department of PathologyUniversity of California San DiegoLa JollaUSA

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