Data from: Detecting adaptive convergent amino acid evolution

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes—including in the presence of a change in the efficacy of selection—and on empirical alignments.diffsel_concat_experimentResults of running diffsel on the concatenation experiment.outdir_without_chains.tarOutput files without diffsel chains.C4AmaranthaceaePolyroot.tar.gzResults of the pipeline on the Amaranthaceae tree.cyp_coding.Chrysithr_root.tar.gzResults of the pipeline on the cyp tree.orthomam_aridity.tar.gzResults of the pipeline on the Orthomam tree annotated with convergence to aridity.orthomam_handpicked.tar.gzResults of the pipeline on the Orthomam tree with branches hand-picked arbitrarily.real_data.tar.gzAnalysis of the Cyperaceae and Amaranthaceae empirical data sets.simulation_details.tar.gzDetails of the simulations used