Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Lanfear, Robert, Australian National University
Calcott, Brett, Australian National University
Ho, Simon Y. W., University of Sydney
Guindon, Stephane, University of Auckland
Published Jan 23, 2012 on Dryad.
Cite this dataset
Lanfear, Robert; Calcott, Brett; Ho, Simon Y. W.; Guindon, Stephane (2012). Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. [Dataset]. Dryad. https://doi.org/10.5061/dryad.fc30r431
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 timeframes, and so permit the objective selection of partitioning schemes even for large multi-locus DNA datasets. We demonstrate that these methods significantly outperform previous approaches, including 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 BIC, AIC, and AICc). 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 .
This file contains all of the input and output files for table 3 in the paper. Including Li et al's alignment file, and partitioning files for all of the different schemes in table 3 of the paper. It also contains the mac-compiled version of RaxML that I used for the analysis, although any version of raxML should work.
There are 10 subfolders, each of which contains a dataset and a partitionfinder.cfg file. The datasets are described in table 1 of the paper, and the results are in table 2. The files in the folders should reproduce all of the results in table 2. All analyses are were run with PartitionFinder v0.9. To download this particular version (which is guaranteed to work with these files, while later
versions might not be) follow this link: . Later versions of PartitionFinder are available here: .