Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
State Key Laboratory of Emerging Infectious Disease and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
Mol Biol Evol. 2020 Feb 1;37(2):599-603. doi: 10.1093/molbev/msz240.
Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.
系统发育树和数据通常以不兼容和不一致的格式存储。包含具有分析结果的树的软件工具的输出通常彼此不兼容，使得难以在比较研究中整合不同分析的结果。treeio 包旨在连接系统发育树输入和输出。它支持提取系统发育树以及常用分析软件的输出。它可以将外部数据与系统发育树联系起来，并合并来自不同来源的树数据，从而能够在进化背景下分析来自不同学科的与系统发育相关的数据。treeio 还支持将具有异质相关数据的系统发育树导出到单个树文件中，包括与 BEAST 兼容的 NEXUS 和 jtree 格式；这有助于数据共享以及文件格式转换，以便下游分析。treeio 包旨在与 tidytree 和 ggtree 包一起使用。可以使用 tidytree 中的 tidy 接口处理树数据，并使用 ggtree 进行可视化。treeio 包在 Bioconductor 和 rOpenSci 项目中发布。可在 https://www.bioconductor.org/packages/treeio/ 获得。
