title: ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes.
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.
authors.affiliation: European Centre for Environment and Human Health, The University of Exeter Medical School, University of Exeter, Truro, United Kingdom. michiel.vos@pcmd.ac.uk
authors.forename: Michiel
authors.initials: M
authors.lastname: Vos
authors.forename: Tim A H
authors.initials: TA
authors.lastname: te Beek
authors.forename: Marc A
authors.initials: MA
authors.lastname: van Driel
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
authors.forename: Adam
authors.initials: A
authors.lastname: Eyre-Walker
authors.forename: Mark W J
authors.initials: MW
authors.lastname: van Passel
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000465:Algorithms; D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D008957:Models, Genetic; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D012984:Software