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#编者信息
熊荣川
明湖实验室
xiongrongchuan@126.com
http://blog.sciencenet.cn/u/Bearjazz
Here we present PhySortR, a fast, flexible R package for screening and sorting phylogenetic trees. The command-line package provides the quick and highly flexible sortTrees function, allowing for screening (within a tree) for “Exclusive” clades that contain only the target leaves and/or “Non-Exclusive” clades that include a defined portion of non-target leaves. Using simulated data, we assess the runtime of PhySortR based on the number of trees and the number of leaves within a tree, and demonstrate the potential of PhySortR in the analysis of multiple, large-scale empirical datasets. | 在这里,我们介绍了PhySortR,一个快速,灵活的R包,用于筛选和分类系统发育树。该R语言包提供快速和高度灵活的树排序功能,允许筛选出(在树中)只包含目标末梢分类单元支系和/或包含所定义的非目标单元支系。利用模拟数据,我们根据树的数量和树内分类单元的数量评估了PhySortR的运行时间,并证明了包提供快速在复合大规模实际数据集分析中的潜力。 |
Stephens T G , Bhattacharya D , Ragan M A , et al. PhySortR: A fast, flexible tool for sorting phylogenetic trees in R[J]. PeerJ, 2016, 4(5):e2038. |
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