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 #  ggtree: an R package for visualization of phylogenetic trees with their annotation data

 
 ```{r echo=FALSE, results="hide", message=FALSE}

 #library("txtplot")

 library("badger")

 library("ypages")

 Biocpkg <- function (pkg) {
     sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
 }
 

 ```
 

 <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

 `r badge_bioc_release("ggtree", "green")`

 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)

 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
 

 <!--
 [![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)
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`
 ` r badge_bioc_download("ggtree", "total", "blue")`
 ` r badge_bioc_download("ggtree", "month", "blue")`
 ` r badge_bioc_download_rank("ggtree")`
 -->

 ```{r comment="", echo=FALSE, results='asis'}
 cat(packageDescription('ggtree')$Description)
 ```

 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)

 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
 

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

 1. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).

    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)

 2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. 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)

 3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. 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).

 ## :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).