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

By Yi Jin, Hong Qian. Ecography, 2019

962 citations recorded by the source corpus.

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.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7bc94f212c36187aedc5fb575ed35010e693eebe

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In Ecology, Evolution, Behavior and Systematics

1. Yi Jin
2. Hong Qian
3. Tao Deng
4. Fabien Leprieur
5. Xianli Wang
6. Hanna Tuomisto
7. D. Jablonski

In Molecular Biology

1. Hong Qian
2. Yi Jin

Citations in the corpus

• Geographic patterns and environmental correlates of taxonomic and phylogenetic beta diversity for large‐scale angiosperm assemblages in China (2020, methodology): “2008) implemented in V.PhyloMaker (scenario 3; Jin and Qian 2019).”
• V.PhyloMaker2: An updated and enlarged R package that can generate very large phylogenies for vascular plants (2022, methodology): “Jin and Qian (2019) updated and expanded this phylogeny by standardizing botanical nomenclature, removing duplicate species, including pteridophyte species from Zanne et al. ’ s (2014) phylogeny, and including those families that are missing from the two phylogenies.”