# treeio: Base classes and functions for phylogenetic tree input and output \[!\[\](https://badges.ropensci.org/179\_status.svg)\](https://github.com/ropensci/onboarding/issues/179) \[!\[Bioc\](http://www.bioconductor.org/shields/years-in-bioc/treeio.svg)\](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#since) \[!\[Project Status: Active - The project has reached a stable, usable state and is being actively developed.\](http://www.repostatus.org/badges/latest/active.svg)\](http://www.repostatus.org/#active) \[!\[platform\](http://www.bioconductor.org/shields/availability/devel/treeio.svg)\](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#archives) \[!\[codecov\](https://codecov.io/gh/GuangchuangYu/treeio/branch/master/graph/badge.svg)\](https://codecov.io/gh/GuangchuangYu/treeio) \[!\[\](https://img.shields.io/badge/release%20version-1.20.2-green.svg)\](https://www.bioconductor.org/packages/treeio) \[!\[\](https://img.shields.io/badge/devel%20version-1.21.3-green.svg)\](https://github.com/guangchuangyu/treeio) \[!\[Linux Travis Build Status\](https://img.shields.io/travis/GuangchuangYu/treeio/master.svg?label=Linux)\](https://travis-ci.org/GuangchuangYu/treeio) \[!\[AppVeyor Build Status\](https://img.shields.io/appveyor/ci/Guangchuangyu/treeio/master.svg?label=Windows)\](https://ci.appveyor.com/project/GuangchuangYu/treeio) \[!\[\](https://img.shields.io/badge/download-284494/total-blue.svg)\](https://bioconductor.org/packages/stats/bioc/treeio) \[!\[\](https://img.shields.io/badge/download-12470/month-blue.svg)\](https://bioconductor.org/packages/stats/bioc/treeio) \[!\[download\](http://www.bioconductor.org/shields/downloads/release/treeio.svg)\](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 for details. \[!\[Twitter\](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)\](https://twitter.com/intent/tweet?hashtags=treeio&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen\_name=guangchuangyu) \[!\[saythanks\](https://img.shields.io/badge/say-thanks-ff69b4.svg)\](https://saythanks.io/to/GuangchuangYu) \[!\[\](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)\](https://yulab-smu.top/images/biobabble.jpg) ## :writing\_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University 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). ## 🏘️ Package Affiliations The \`treeio\` package is a part of the Bioconductor and rOpenSci projects. | \[!\[bioconductor\_footer\](http://bioconductor.org/images/logo\_bioconductor.gif)\](http://bioconductor.org) | \[!\[ropensci\_footer\](http://ropensci.org/public\_images/github\_footer.png)\](http://ropensci.org) | |:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|
\[!\[\](https://badges.ropensci.org/179\_status.svg)\](https://github.com/ropensci/onboarding/issues/179) \[!\[Bioc\](http://www.bioconductor.org/shields/years-in-bioc/treeio.svg)\](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#since) \[!\[Project Status: Active - The project has reached a stable, usable state and is being actively developed.\](http://www.repostatus.org/badges/latest/active.svg)\](http://www.repostatus.org/#active) \[!\[platform\](http://www.bioconductor.org/shields/availability/devel/treeio.svg)\](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#archives) \[!\[codecov\](https://codecov.io/gh/GuangchuangYu/treeio/branch/master/graph/badge.svg)\](https://codecov.io/gh/GuangchuangYu/treeio) \[!\[\](https://img.shields.io/badge/release%20version-1.20.2-green.svg)\](https://www.bioconductor.org/packages/treeio) \[!\[\](https://img.shields.io/badge/devel%20version-1.21.3-green.svg)\](https://github.com/guangchuangyu/treeio) \[!\[Linux Travis Build Status\](https://img.shields.io/travis/GuangchuangYu/treeio/master.svg?label=Linux)\](https://travis-ci.org/GuangchuangYu/treeio) \[!\[AppVeyor Build Status\](https://img.shields.io/appveyor/ci/Guangchuangyu/treeio/master.svg?label=Windows)\](https://ci.appveyor.com/project/GuangchuangYu/treeio) \[!\[\](https://img.shields.io/badge/download-284494/total-blue.svg)\](https://bioconductor.org/packages/stats/bioc/treeio) \[!\[\](https://img.shields.io/badge/download-12470/month-blue.svg)\](https://bioconductor.org/packages/stats/bioc/treeio) \[!\[download\](http://www.bioconductor.org/shields/downloads/release/treeio.svg)\](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 for details. \[!\[Twitter\](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)\](https://twitter.com/intent/tweet?hashtags=treeio&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen\_name=guangchuangyu) \[!\[saythanks\](https://img.shields.io/badge/say-thanks-ff69b4.svg)\](https://saythanks.io/to/GuangchuangYu) \[!\[\](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)\](https://yulab-smu.top/images/biobabble.jpg) ## :writing\_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University 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). ## 🏘️ Package Affiliations The \`treeio\` package is a part of the Bioconductor and rOpenSci projects. | \[!\[bioconductor\_footer\](http://bioconductor.org/images/logo\_bioconductor.gif)\](http://bioconductor.org) | \[!\[ropensci\_footer\](http://ropensci.org/public\_images/github\_footer.png)\](http://ropensci.org) | |:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|