<!-- README.md is generated from README.Rmd. Please edit that file --> # treeio: Base classes and functions for phylogenetic tree input and output <a href="https://yulab-smu.top/treedata-book/"><img src="man/figures/logo.png" align="right" height="139" /></a> [](https://github.com/ropensci/onboarding/issues/179) [](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#since) [](http://www.repostatus.org/#active) [](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#archives) [](https://codecov.io/gh/GuangchuangYu/treeio) [](https://www.bioconductor.org/packages/treeio) [](https://github.com/guangchuangyu/treeio) [](https://travis-ci.org/GuangchuangYu/treeio) [](https://ci.appveyor.com/project/GuangchuangYu/treeio) [](https://bioconductor.org/packages/stats/bioc/treeio) [](https://bioconductor.org/packages/stats/bioc/treeio) [](https://bioconductor.org/packages/stats/bioc/treeio) ‘treeio’ is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats. Visit <https://yulab-smu.top/treedata-book/> for details. [](https://twitter.com/intent/tweet?hashtags=treeio&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [](https://saythanks.io/to/GuangchuangYu) [](https://yulab-smu.top/images/biobabble.jpg) ## :writing_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <https://yulab-smu.top> If you use [treeio](http://bioconductor.org/packages/treeio) in published research, please cite: - LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, **G Yu**^\*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. ***Molecular Biology and Evolution***. 2020, 37(2):599-603. doi: [10.1093/molbev/msz240](http://dx.doi.org/10.1093/molbev/msz240). ## :arrow_double_down: Installation Get the released version from Bioconductor: ``` r ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") ## BiocManager::install("BiocUpgrade") ## you may need this BiocManager::install("treeio") ``` Or the development version from github: ``` r ## install.packages("devtools") devtools::install_github("YuLab-SMU/treeio") ``` ## :sparkling_heart: Contributing We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md). ## :houses: Package Affiliations The `treeio` package is a part of the Bioconductor and rOpenSci projects. | [](http://bioconductor.org) | [](http://ropensci.org) | |:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|