Partition FinderΒΆ

PartitionFinder2 is a program for selecting best-fit partitioning schemes and models of evolution for nucleotide, amino acid, and morphology alignments. The user provides an alignment, and optionally some pre-defined data blocks (e.g. 9 data blocks defining the 1st, 2nd and 3rd codon positions of 3 protein-coding genes, see Figure 1). The program then finds the best partitioning scheme for this dataset, at the same time as selecting best-fit models for each subset of sites/columns. Here are a few things you can do with the program:

  1. Find the best-fit partitioning scheme nucleotide, amino acid, or morphology datasets
  2. Compare any number of user-defined partitioning schemes
  3. Find best-fit models of evolution for each subset in any partitioned dataset (much like you might do with ModelTest or ProtTest).