PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Evolutionary Studies
- Keywords
- phylogenetics, phylogenomics, tree sorting, phylogenetic trees
- Copyright
- © 2015 Stephens et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ PrePrints 3:e1609v1 https://doi.org/10.7287/peerj.preprints.1609v1
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.
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.