PhySortR

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.

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

PhySortR is an R package to screen and sort phylogenetic trees.

PhySortR

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