PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

TLDR

PartitionFinder 2 is a program for automatically selecting best‑fit partitioning schemes and models of evolution for phylogenetic analyses. It supports morphological and genome‑scale datasets, offers new output formats for downstream software, includes many new molecular evolution models, and runs on Windows, OSX, and Linux under an open‑source license. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. It can be downloaded from www.robertlanfear.com/partitionfinder and the source code is available at https://github.com/brettc/partitionfinder.

Abstract

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.