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partitionfinder website  

PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you wish to compare or select partitioning schemes or models of molecular evolution. Both programs come together as a single download. Click below to get the appropriate download for your system.

Environment Modules

Run module spider partitionfinder to find out what environment modules are available for this application.

System Variables

  • HPC_PARTITIONFINDER_DIR - installation directory

How To Run

Run PartitionFinder programs for nt or aa model analysis respectively as -p X DIRECTORY


once the partitionfinder module is loaded where "X" is the number of compute cores requested in the job script and "DIRECTORY" is the full path to a folder containing a configuration file (partition_finder.cfg) and a nucleotide or aminoacid alignment in Phylip format.


If you publish research that uses partitionfinder you have to cite it as follows: Please cite Lanfear et al. (2012) if you use the tool for published research.