MonoPhy: A simple R package to find and visualize monophyly issues
MonoPhy: A simple R package to find and visualize monophyly issues
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MonoPhy：一个简单的 R 包，用于查找和可视化单系问题
DOI：
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
B. O’Meara
中科院分区：
文献类型：
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作者：
Orlando Schwery;B. O’Meara
背景分类单元的单系性是系统发育树的一个重要属性。缺乏它可能暗示了树或当前分类学的缺陷，或者可能表明谱系分类不完整或水平基因转移的情况。不管原因是什么，缺乏单系性会误导随后的分析。虽然单系性在概念上很简单，但要评估数百到数千个物种的现代单系性，人工操作是繁琐和耗时的。结果R软件包MonoPhy允许评估和探索单系分类群中的单系性。它可以仅使用系统发育来评估属的单系性，并且通过额外的输入文件，还可以检查任何其他所需的更高级分类单元或未排名的组。结论摘要表，易于subsettable结果和几个可视化选项允许快速方便地探索单系问题，从而使MonoPhy成为任何研究人员与遗传学合作的宝贵工具。生物信息学，计算生物学
Background. The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species. Results. The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny. It can assess themonophyly of genera using the phylogeny only, and with an additional input file any other desired higher order taxa or unranked groups can be checked as well. Conclusion. Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus makingMonoPhy a valuable tool for any researcher working with phylogenies. Subjects Bioinformatics, Computational Biology