2022Acta Botanica YunnanicaOpen access

U.PhyloMaker: An R package that can generate large phylogenetic trees for plants and animals

Yi Jin, Hong Qian

Open full text 188 citations

Abstract

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

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What this paper is about

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

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Available abstract

The previously released packages of the PhyloMaker series (i.e. S.PhyloMaker, V.PhyloMaker, and V.PhyloMaker2) have been broadly used to generate phylogenetic trees for ecological and biogeographical studies. Although these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available, they focus on generating phylogenetic trees for plants based on the megatrees provided by the packages. How to use these packages to generate phylogenetic trees based on other megatrees is not straightforward. Here, we present a new tool, which is called 'U.PhyloMaker', and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

Key concepts: Phylogenetic tree, Phylogenetic relationship, Biology, Phylogenetic network, Phylogenetics, Tree (set theory), R package, Evolutionary biology

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