PhyloMAd: efficient assessment of phylogenomic model adequacy.

Abstract

Statistical phylogenetic inference plays an important role in evolutionary biology. The accuracy of phylogenetic methods relies on having suitable models of the evolutionary process. Various tools allow comparisons of candidate phylogenetic models, but assessing the absolute performance of models remains a considerable challenge. We introduce PhyloMAd, a user-friendly application for assessing the adequacy of commonly used models of nucleotide substitution and among-lineage rate variation. Our software implements a fast, likelihood-based method of model assessment that is tractable for analyses of large multi-locus datasets. PhyloMAd provides a means of informing model improvement, or selecting data to enhance the evolutionary signal in phylogenomic analyses. PhyloMAd, together with a manual, a tutorial and the source code, are freely available from the GitHub repository github.com/duchene/phylomad.