title: PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.
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.
authors.affiliation: ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, University of Queensland , Brisbane, Queensland , Australia.
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Stephens
authors.affiliation: Department of Ecology, Evolution and Natural Resources, Rutgers University , New Brunswick, NJ , USA.
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.affiliation: ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, University of Queensland , Brisbane, Queensland , Australia.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ragan
authors.affiliation: ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, University of Queensland , Brisbane, Queensland , Australia.
authors.forename: Cheong Xin
authors.initials: CX
authors.lastname: Chan
keywords: phylogenetic trees; phylogenetics; phylogenomics