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<!-- README.md is generated from README.Rmd. Please edit that file -->
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-ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-===========================================================================================================================
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+# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[](https://bioconductor.org/packages/ggtree) [](https://github.com/guangchuangyu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://awesome-r.com/#awesome-r-graphic-displays)
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+[](https://bioconductor.org/packages/ggtree)
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+[](https://github.com/guangchuangyu/ggtree)
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+[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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+[](https://awesome-r.com/#awesome-r-graphic-displays)
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-[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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+[](http://www.repostatus.org/#active)
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+[](https://codecov.io/gh/GuangchuangYu/ggtree)
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+[](https://github.com/GuangchuangYu/ggtree/commits/master)
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-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.
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+The `ggtree` package extending the `ggplot2` package. It based on
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+grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
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+is designed for not only viewing phylogenetic tree but also displaying
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+annotation data on the tree.
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-For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
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+For details, please visit our project website,
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+<https://guangchuangyu.github.io/software/ggtree>.
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-- [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
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-- [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
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-- [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
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-- [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
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+ - [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
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+ - [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
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+ - [Featured
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+ Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
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+ - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
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-[](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [](https://saythanks.io/to/GuangchuangYu) [](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
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+[](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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+[](https://saythanks.io/to/GuangchuangYu)
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+[](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
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+[](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
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+-----
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Please cite the following article when using `ggtree`:
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-**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.
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+**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
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+package for visualization and annotation of phylogenetic trees with
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+their covariates and other associated data. ***Methods in Ecology and
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+Evolution***. 2017,
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+8(1):28-36.
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-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079)
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+[](http://dx.doi.org/10.1111/2041-210X.12628)
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+-----
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### Citation
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### Download stats
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-[](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[](https://bioconductor.org/packages/stats/bioc/ggtree)
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<img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
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-Contributing
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+## Contributing
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-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).
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+We welcome any contributions\! By participating in this project you
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+agree to abide by the terms outlined in the [Contributor Code of
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+Conduct](CONDUCT.md).
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