PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

Stephens, Timothy, Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2016) PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4 e2038.1-e2038.13. doi:10.7717/peerj.2038

Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads
Stephens2016_PeerJ.pdf Full text (open access) application/pdf 2.07MB 0

Author Stephens, Timothy
Bhattacharya, Debashish
Ragan, Mark A.
Chan, Cheong Xin
Title PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Journal name PeerJ   Check publisher's open access policy
ISSN 2167-8359
Publication date 2016-05-12
Year available 2016
Sub-type Article (original research)
DOI 10.7717/peerj.2038
Open Access Status DOI
Volume 4
Start page e2038.1
End page e2038.13
Total pages 13
Place of publication London, United Kingdom
Publisher PeerJ
Collection year 2017
Language eng
Formatted abstract
A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.
Keyword Phylogenetics
Phylogenetic trees
Computational biology
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Institute for Molecular Bioscience - Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 1 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 0 times in Scopus Article
Google Scholar Search Google Scholar
Created: Tue, 12 Jul 2016, 16:52:47 EST by Cheong Xin Chan on behalf of Institute for Molecular Bioscience