ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes

This is the final version of the article. Available from the publisher via the DOI in this record.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.MWJvP is funded by the Netherlands Organization for Scientific Research (NWO) via a VENI grant. TtB and MAvD are funded by the BioAssist/BRS programme of the Netherlands Bioinformatics Centre, which is supported by the Netherlands Genomics Initiative. This work is part of the programme of BiG Grid, the Dutch e-Science Grid, which is financially supported by the NWO. MV is supported by investment from the European Regional Development Fund and the European Social Fund Convergence Programme for Cornwall and the Isles of Scilly to the European Centre for the Environment and Human Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript