V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants

11 March 2019

Jin, Yi; Qian, Hong

We present V.PhyloMaker, a freely available package for R designed to generate phylogenies for vascular plants. The mega-tree implemented in V.PhyloMaker (i.e., GBOTB.extended.tre), which was derived from two recently published mega-trees and includes 74,533 species and all families of extant vascular plants, is the largest dated phylogeny for vascular plants. V.PhyloMaker can generate phylogenies for very large species lists (the largest species list that we tested included 314,686 species). V.PhyloMaker generates phylogenies at a fast speed, much faster than other phylogeny-generating packages. Our tests of V.PhyloMaker show that generating a phylogeny for 60,000 species requires less than six hours. V.PhyloMaker includes an approach to attach genera or species to their close relatives in a phylogeny. We provide a simple example in this paper to show how to use V.PhyloMaker to generate phylogenies.