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

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Listed:
  • Michiel Vos
  • Tim A H te Beek
  • Marc A van Driel
  • Martijn A Huynen
  • Adam Eyre-Walker
  • Mark W J van Passel

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.

Suggested Citation

  • Michiel Vos & Tim A H te Beek & Marc A van Driel & Martijn A Huynen & Adam Eyre-Walker & Mark W J van Passel, 2013. "ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-4, May.
    • Handle: RePEc:plo:pone00:0062447
    DOI: 10.1371/journal.pone.0062447
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