ModelFinder: fast model selection for accurate phylogenetic estimates

Abstract

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space. Model-based molecular phylogenetic analysis plays a key role in comparative genomics and evolutionary biology, allowing us to annotate genomes more accurately1, test our understanding of the evolution of species, genomes and genes2–6, and determine the likely origins and routes of dispersal of pathogens and pests7,8. Selecting an optimal model of sequence evolution (SE) is a critical step in all such analyses. Here we introduce ModelFinder, a model-selection method that combines substitution models used in other popular model-selection methods9,10 with a flexible rate-heterogeneity-across-sites (RHAS) Show more