PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
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Author and article information
Abstract
A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, such as robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for sorting phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa, with customisable options to assess clades within the context of the whole tree. PhySortR is a command-line tool that is freely available, highly scalable, and easily automatable.
Cite this as
2015. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ PrePrints 3:e1609v1 https://doi.org/10.7287/peerj.preprints.1609v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a preprint submission to PeerJ Preprints. This manuscript version has been submitted for consideration of publication in a peer-reviewed journal.
Sections
Supplemental Information
Supplementary Figure S1: Tree-sorting algorithm in PhySortR
Supplementary Figure S2: Arguments within sortTrees function in PhySortR
Supplementary Data S1: Simulated trees with varying N at fixed X = 100
Supplementary Data S2: Simulated trees with varying X at fixed N = 1000
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Timothy G Stephens conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Debashish Bhattacharya contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Mark A Ragan contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Cheong Xin Chan conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
Source code and manual of this toolkit are available from Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/PhySortR/
Funding
This work was supported by the Australian Research Council Discovery Project (DP150101875) grant awarded to M.A.R., C.X.C, and D.B. C.X.C. is supported by Great Barrier Reef Foundation Bioinformatics Fellowship awarded to M.A.R. D.B. acknowledges support from the National Science Foundation (1004213). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.