Download PartitionFinder

PartitionFinder icon 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.

PF for Windows


for Windows

PF for Windows
PF for Macs


for Mac OS X

PF for Macs

Additional Resources

Google Group

Questions, suggestions, problems, or feedback? Visit the PartitionFinder google group, or alternatively just email me.


For a detailed step-by-step tutorial for running PartitionFinder and interpreting the output, see the PartitionFinder tutorial here.


For updates on new versions, releases, features, and bug fixes please visit the News page here.

Manual PDF

The manual comes with the download. In case you need another copy though, it's here


Lanfear et al. (2012) describes PartitionFinder. Please cite it if you use PartitionFinder.


If you're stuck and the manual doesn't help, try looking here first.

Old Versions

Every released version of PartitionFinder is available from the GitHub repository here:


Click here to see the Google Scholar link for who has cited PartitionFinder, and read the papers to see how other people use the program.


I keep a public collection of curated Partitioned Alignments, along with PartitionFinder configuration files. Feel free to contribute, or use them as you wish.

Partition Finder