rtrees: an R package to assemble phylogenetic trees from megatrees
rtrees: an R package to assemble phylogenetic trees from megatrees
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DOI：
10.1111/ecog.06643
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发表时间：
2023-04
期刊：
影响因子：
5.9
通讯作者：
Daijiang Li
中科院分区：
文献类型：
--
作者：
Daijiang Li
尽管越来越多的可用多个分类群的系统发育假说，他们中的大多数并不包括所有的物种。在系统发育生态学中，仍然强烈要求在一项研究中包括所有物种的系统发育。现有的软件工具，嫁接物种的骨干巨树，但是，大多数是有限的，以一个特定的分类组，如植物或鱼类。在这里，我将介绍一个新的用户友好的R包，'rtrees'，它可以从现有的或用户提供的megatree中组装子树。对于大多数常见的分类群，用户只能提供一个物种科学名称的向量，以获得一个系统发生或一组后验系统发生。我希望rtrees能提供一个简单、灵活、可靠的方法来组装巨型树的系统发育，促进系统发育生态学的发展。
Despite the increasingly available phylogenetic hypotheses for multiple taxonomic groups, most of them do not include all species. In phylogenetic ecology, there is still a strong demand to have phylogenies with all species in a study included. The existing software tools to graft species to backbone megatrees, however, are mostly limited to a specific taxonomic group such as plants or fishes. Here, I introduce a new user‐friendly R package, ‘rtrees', that can assemble phylogenies from existing or user‐provided megatrees. For most common taxonomic groups, users can only provide a vector of species scientific names to get a phylogeny or a set of posterior phylogenies from megatrees. It is my hope that ‘rtrees' can provide an easy, flexible, and reliable way to assemble phylogenies from megatrees, facilitating the progress of phylogenetic ecology.