Rader Jonathan A, Pivovarnik Madelyn A, Vantilburg Matias E, Whitehouse Logan S
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, United States.
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7264, United States.
Bioinform Adv. 2023 Oct 5;3(1):vbad144. doi: 10.1093/bioadv/vbad144. eCollection 2023.
Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of the National Center for Biotechnology Information Taxonomy and Global Biodiversity Information Facility databases to find associated synonyms with given target species names.
PhyloMatcher is easily installed as a Python package with pip, or as a standalone GUI application. PhyloMatcher source code and documentation are freely available at https://github.com/Lswhiteh/PhyloMatcher, the GUI application can be downloaded from the Releases page.
大规模比较研究依赖于系统发育树和表型数据的应用，这两者都来自多种来源，但由于系统发育分类的性质随时间变化，比较数据集中的许多分类单元名称与系统发育树中的命名法不匹配。在大型比较数据集中手动整理分类同义词可能令人生畏。为了解决这个问题，我们引入了PhyloMatcher，这是一种工具，它允许以编程方式查询美国国立生物技术信息中心分类法和全球生物多样性信息设施数据库，以找到与给定目标物种名称相关的同义词。
PhyloMatcher可以很容易地通过pip作为Python包安装，也可以作为独立的图形用户界面应用程序安装。PhyloMatcher的源代码和文档可在https://github.com/Lswhiteh/PhyloMatcher上免费获取，图形用户界面应用程序可从发布页面下载。
