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

Background Upon phylogenetic data, coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes that are likely to be associated with trait variation. 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 http://github.com/linudz/caastools, along with documentation and examples. Supplementary information Supplementary data are available.