CAAStools, a toolbox to identify and test Convergent Amino Acid Substitutions.

BackgroundCoincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for pre-defined groups of species representing the phenotypic values targeted by the user. Implementation and availabilityCAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples. Supplementary informationSupplementary data are available.