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

Mol Biol Evol. 2017 Mar 1;34(3):772-773. doi: 10.1093/molbev/msw260.


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 The source code is available at

Keywords: AIC; AICc; BIC; model selection; molecular evolution.; partitioning.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Biological Evolution
  • Computer Simulation
  • Evolution, Molecular*
  • Genome
  • Models, Genetic*
  • Phylogeny
  • Sequence Analysis, DNA / methods*
  • Software