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

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 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
 grammar of graphics. ‘ggtree’ is designed for visualization and

 annotation of phylogenetic trees and other tree-like structures with
 their annotation data.

 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>
 

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 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**. 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**<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)

 3.  **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).

 ## :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).