PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
Open accessAbstract
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
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Standard phylogenomic analyses typically partition datasets by genes or sets of genes, with each partition having a separate model, rather than applying a single site-homogeneous model to an entire supermatrix.
“For example, it has been pointed out11,12,34 that standard phylogenomic analyses do not typically apply a single site-homogeneous model to an entire supermatrix, but rather partition datasets by genes, or by sets of genes (as merged under an optimality criterion)36,37, with each partition having a separate model.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [37]
Protein evolution is not homogeneous.
“However, protein evolution is not homogeneous.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [24]
Different proteins can have their own protein-specific replacement rates.
“different proteins can have their own protein-specific replacement rates (e.g., [24])”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [24]
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- Authors
- Lanfear, R., Calcott, B., Ho, S. Y. W., & Guindon, S.
- Affiliations
- Australian National University (AU)
- The University of Sydney (AU)
- University of Auckland (NZ)
- Corresponding author
- Lanfear, R.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-01-20
- Volume
- 29
- Issue
- 6
- Pages
- 1695-1701
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2133870991
- Cited by
- 5,732
- References
- 1
- Citations by year
- 2026: 128 · 2025: 221 · 2024: 276 · 2023: 293 · 2022: 376 · 2021: 514 · 2020: 530 · 2019: 548 · 2018: 662 · 2017: 705 · 2016: 608 · 2015: 429 · 2014: 307 · 2013: 120 · 2012: 10
- FWCI
- 111.25
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- ANU Open Research (Australian National University) (submittedVersion)
- Funders
- Marsden Fund (08-UOA-068)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- PartitionFinder, partitioning schemes, nucleotide substitution models, model selection, molecular evolution, phylogenetic inference, information-theoretic metrics, Bayesian information criterion, Akaike information criterion
- MeSH terms
- Algorithms, Bayes Theorem, Models, Genetic, Phylogeny, Selection, Genetic, Software, Cluster Analysis, Likelihood Functions, Sequence Analysis, DNA, Evolution, Molecular
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