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

IF 4.6 1区生物学 Q1 PLANT SCIENCES

Plant Diversity Pub Date : 2023-05-01 DOI:10.1016/j.pld.2022.12.007

Yi Jin , Hong Qian

引用次数: 15

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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一个R软件包，可以为植物和动物生成大型的系统发育树

先前发布的PhyloMaker系列软件包（即S.PhyloMaker、V.PhyloMaker和V.PhyloMaker2）已被广泛用于生成用于生态和生物地理学研究的系统发育树。尽管这些软件包可以用于为任何有巨树可用的动植物群体生成系统发育树，但它们专注于基于软件包提供的巨树为植物生成系统发育图。如何使用这些软件包在其他巨树的基础上生成系统发育树并不简单。在这里，我们介绍了一个名为“U.PhyloMaker”的新工具，以及一个简单的R脚本，该脚本可用于以相对较快的速度轻松生成植物和动物的大型系统发育树。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant Diversity Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics

CiteScore

8.30

自引率

6.20%

发文量

1863

审稿时长

35 days

期刊介绍： Plant Diversity (formerly Plant Diversity and Resources) is an international plant science journal that publishes substantial original research and review papers that advance our understanding of the past and current distribution of plants, contribute to the development of more phylogenetically accurate taxonomic classifications, present new findings on or insights into evolutionary processes and mechanisms that are of interest to the community of plant systematic and evolutionary biologists. While the focus of the journal is on biodiversity, ecology and evolution of East Asian flora, it is not limited to these topics. Applied evolutionary issues, such as climate change and conservation biology, are welcome, especially if they address conceptual problems. Theoretical papers are equally welcome. Preference is given to concise, clearly written papers focusing on precisely framed questions or hypotheses. Papers that are purely descriptive have a low chance of acceptance. Fields covered by the journal include: plant systematics and taxonomy- evolutionary developmental biology- reproductive biology- phylo- and biogeography- evolutionary ecology- population biology- conservation biology- palaeobotany- molecular evolution- comparative and evolutionary genomics- physiology- biochemistry