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# ggtree: an R package for visualization of phylogenetic trees with their annotation data
<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>
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
[](https://www.bioconductor.org/packages/ggtree)
[](https://codecov.io/gh/GuangchuangYu/ggtree)
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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.top/treedata-book/>.
## :writing\_hand: Authors
Guangchuang YU
School of Basic Medical Sciences, Southern Medical University
<https://guangchuangyu.github.io>
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[](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**. 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).
