ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

M. Vos, T.A.H. Beek, M.A. van Driel, M.A. Huynen, A. Eyre-Walker, M.W.J. van Passel

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8 Citations (Scopus)

Abstract

Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl
Original languageEnglish
Article numbere62447
JournalPLoS ONE
Volume8
Issue number5
DOIs
Publication statusPublished - 2013

Keywords

  • positive selection
  • evolution
  • recombination
  • drosophila
  • campylobacter

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    Vos, M., Beek, T. A. H., van Driel, M. A., Huynen, M. A., Eyre-Walker, A., & van Passel, M. W. J. (2013). ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes. PLoS ONE, 8(5), [e62447]. https://doi.org/10.1371/journal.pone.0062447