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PartitionFinder specifications


Unique identifier OMICS_29418
Name PartitionFinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.1
Stability Stable
numpy, pandas, pytables, pyparsing, scipy, sklearn
Maintained Yes




No version available



  • person_outline Robert Lanfear

Additional information

Publications for PartitionFinder

PartitionFinder citations


The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] oth nucleotide (ND) and amino acid (AAD) sequences of the PCGs, which were partitioned by genes and by codon positions. To select the best-fitting partitioning scheme and models of evolution, we used PartitionFinder v2, with the settings: (i) unlink branch lengths and (ii) use the corrected Akaike information criterion (AICc) for model selection. ML and BI analyses were performed using the RAxML w […]


Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

BMC Genomics
PMCID: 5946542
PMID: 29747572
DOI: 10.1186/s12864-018-4717-7
call_split See protocol

[…] of their heterogeneous base composition and poor phylogenetic performance [, ]. For each dataset, best fit combinations of partitioning schemes and nucleotide substitution models were determined with PartitionFinder version 2.1.1 [], using the “greedy” algorithm [] and the Bayesian information criterion (BIC), with the branch lengths of alternative partitions linked and with the software set to ev […]


Conservation systematics of the shield backed trapdoor spiders of the nigrum group (Mygalomorphae, Idiopidae, Idiosoma): integrative taxonomy reveals a diverse and threatened fauna from south western Australia

PMCID: 5956031
PMID: 29773959
DOI: 10.3897/zookeys.756.24397

[…] ameters (Katoh and Standley 2013). Individual alignments for the seven genes were concatenated to generate the FULL 82 taxon dataset (Suppl. material ) which included all available data for all taxa. PartitionFinder Version 1.1.1 () was used to choose an optimal partitioning scheme, favouring a 14-partition model for the FULL dataset. The COI dataset (Suppl. materials , ) was visualised with a Tam […]


Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] 7.205. Phylogenetic relationships were reconstructed with MrBayes version 3.2.5, IQ-TREE web server and PhyloBayes-MPI. In MrBayes analyses, matrices were partitioned by codon position. Then, we used PartitionFinder version 1.1.1 to determine the best partition and substitution models. Four independent Markov chains were run for 10 million metropolis-coupled generations, with tree sampling every 1 […]


Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago

BMC Genomics
PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] bp of sequence data. To account for rate heterogeneity among genes, the dataset was partitioned into subsets of genes evolving under the same evolutionary model and with similar substitution rates in PartitionFinder version 2.1.1 []. Bayesian information criterion (BIC) was used for model selection, and branch lengths between partitions were allowed to be unlinked. We tested only for partitioning […]


Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas

Sci Rep
PMCID: 5917027
PMID: 29695730
DOI: 10.1038/s41598-018-24497-7
call_split See protocol

[…] l in BEAST 2.4.6 to infer demographic changes within the last centuries in Grauer’s and mountain gorillas. The best partition scheme and the best fitting model for each partition were identified with PartitionFinder 2, only considering models available in the BEAST 2 software package. The skyline analysis was then run for both subspecies separately under a strict molecular clock model using the in […]


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PartitionFinder institution(s)
Research School of Biology, Australian National University, Canberra, ACT, Australia; Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia; Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA; Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA; Department of Philosophy, University of Sydney, Sydney, NSW, Australia
PartitionFinder funding source(s)
Supported by the Australian Research Council, NSF DEB-1256993 and the Macquarie University Genes to Geoscience center.

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