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

doi:10.1016/j.pld.2022.12.007

Plant Diversity ›› 2023, Vol. 45 ›› Issue (03): 347-352.DOI: 10.1016/j.pld.2022.12.007

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

Yi Jin^a, Hong Qian^b

a. Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China;
b. Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, IL 62703, USA

Received:2022-11-19 Revised:2022-12-16 Online:2023-07-06
Contact: Yi Jin,E-mail:codon@126.com;Hong Qian,E-mail:hong.qian@illinoisstatemuseum.org
Supported by:
We are grateful to Shenhua Qian, Jian Zhang, and Yadong Zhou for testing U.PhyloMaker and anonymous reviewers for their comments. This work was supported by the Natural Science and Technology Foundation of Guizhou Province [[2020]1Z013] (to Y.J.); and the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province [U1812401] (to Y.J.).

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

Yi Jin^a, Hong Qian^b

a. Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China;
b. Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, IL 62703, USA

通讯作者: Yi Jin,E-mail:codon@126.com;Hong Qian,E-mail:hong.qian@illinoisstatemuseum.org
基金资助:
We are grateful to Shenhua Qian, Jian Zhang, and Yadong Zhou for testing U.PhyloMaker and anonymous reviewers for their comments. This work was supported by the Natural Science and Technology Foundation of Guizhou Province [[2020]1Z013] (to Y.J.); and the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province [U1812401] (to Y.J.).

Abstract

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 words: Animals, Community phylogenetics, Megatree, Phylogeny, Plants, Species list

摘要： 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.

关键词: Animals, Community phylogenetics, Megatree, Phylogeny, Plants, Species list

Yi Jin, Hong Qian. U.PhyloMaker:An R package that can generate large phylogenetic trees for plants and animals[J]. Plant Diversity, 2023, 45(03): 347-352.

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

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

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