ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes
Open Access
- 6 May 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (5) , e62447
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.Keywords
This publication has 22 references indexed in Scilit:
- Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniaeBMC Ecology and Evolution, 2011
- Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species ConceptGenome Biology and Evolution, 2010
- Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypesBMC Ecology and Evolution, 2009
- Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus CampylobacterGenome Research, 2009
- Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial GenomesMolecular Biology and Evolution, 2008
- The Emergence and Fate of Horizontally Acquired Genes in Escherichia coliPLOS Computational Biology, 2008
- PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution, 2007
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003
- Adaptive protein evolution at the Adh locus in DrosophilaNature, 1991