<!-- 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" /> [![releaseVersion](https://img.shields.io/badge/release%20version-1.12.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.2-green.svg?style=flat)](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-2018--07--19-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 our project website, <https://guangchuangyu.github.io/software/ggtree>. - [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/) - [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/) - [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/) - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback) [![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-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png) ------------------------------------------------------------------------ Please cite the following article when using `ggtree`: **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](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-320-green.svg?style=flat)](https://www.altmetric.com/details/10533079) ------------------------------------------------------------------------ ### Citation <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/> ### Download stats [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-31843/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1325/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/> 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).