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Methods Mol Biol. 2009;537:163-83. doi: 10.1007/978-1-59745-251-9_8.

Detecting signatures of selection from DNA sequences using Datamonkey.

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Antiviral Research Center, Department of Pathology, University of California San Diego, La Jolla, CA, USA.


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 ( 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.

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