CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions

Background Coincidence 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 availability CAAStools source code is available at , along with documentation and examples. Supplementary information Supplementary data are available. ### Competing Interest Statement The authors have declared no competing interest.