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

PeerJ

article

Timothy G. Stephens¹  Debashish Bhattacharya²  Mark A. Ragan¹  Cheong Xin Chan¹ 

[1] ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, University of Queensland;Department of Ecology, Evolution and Natural Resources, Rutgers University

关键词: phylogenetics;    phylogenomics;    phylogenetic trees;   

DOI  :  10.7717/peerj.2038

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY