rgenesconverged : An R Package for the Exploration of Molecular Convergent Evolution

Abstract

Sequence convergence is a type of convergent evolution that results in similarity between orthologous genetic sequences. However, this can be difficult to evaluate statistically given classical paradigms for convergent evolution, which rest on the assumption that convergent phenotypes are achieved by unrelated genetic mechanisms. While sophisticated models exist to model this process and to evaluate the probability of this explanation of genetic similarity across two different species, no tool has currently been implemented in R to carry out these analyses. Here we present rgenesconverged, an R package allowing the exploration of sequence convergence hypotheses in a given phylogeny.