<!-- README.md is generated from README.Rmd. Please edit that file --> # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> [![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![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) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. For details, please visit <https://yulab-smu.github.io/treedata-book/>. ## :writing\_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <https://guangchuangyu.github.io> [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&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://guangchuangyu.github.io/blog_images/biobabble.jpg) If you use [ggtree](http://bioconductor.org/packages/ggtree) in published research, please cite the most appropriate paper(s) from this list: 1. **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two methods for mapping and visualizing associated data on phylogeny using ggtree. ***Molecular Biology and Evolution***, 2018, 35(2):3041-3043. doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194). - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data) 2. **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36. doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628). <img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/> [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/> ## :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).