README.Rmd

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#  treeio: Base classes and functions for phylogenetic tree input and output <a href="https://yulab-smu.top/treedata-book/"><img src="man/figures/logo.png" align="right" height="139" /></a>

```{r echo=FALSE, results="hide", message=FALSE}
#library("txtplot")
library("badger")
library("ypages")

library("yulab.utils")
```

[![](https://badges.ropensci.org/179_status.svg)](https://github.com/ropensci/onboarding/issues/179)
[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/treeio.svg)](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#since)
[![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)
[![platform](http://www.bioconductor.org/shields/availability/devel/treeio.svg)](https://www.bioconductor.org/packages/devel/bioc/html/treeio.html#archives)
[![codecov](https://codecov.io/gh/GuangchuangYu/treeio/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/treeio)


`r badge_bioc_release("treeio", "green")`
`r badge_devel("guangchuangyu/treeio", "green")`
[![Linux Travis Build Status](https://img.shields.io/travis/GuangchuangYu/treeio/master.svg?label=Linux)](https://travis-ci.org/GuangchuangYu/treeio)
[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/treeio/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/treeio)


`r badge_bioc_download("treeio", "total", "blue")`
`r badge_bioc_download("treeio", "month", "blue")`
`r badge_bioc_download_rank("treeio")`



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

Visit <https://yulab-smu.top/treedata-book/> for details.


[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=treeio&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://yulab-smu.top/images/biobabble.jpg")`




## :writing_hand: Authors

Guangchuang YU 

School of Basic Medical Sciences, Southern Medical University

<https://yulab-smu.top>

If you use `r Biocpkg('treeio')` in published research, please cite:

+ LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, __G Yu__^\*^. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. __*Molecular Biology and Evolution*__. 2020, 37(2):599-603. doi: [10.1093/molbev/msz240](http://dx.doi.org/10.1093/molbev/msz240).


## :arrow_double_down: Installation

Get the released version from Bioconductor:

```r
## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("treeio")
```

Or the development version from github:

```r
## install.packages("devtools")
devtools::install_github("YuLab-SMU/treeio")
```



## :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).


## :houses: Package Affiliations

The `treeio` package is a part of the Bioconductor and rOpenSci projects.

| [![bioconductor_footer](http://bioconductor.org/images/logo_bioconductor.gif)](http://bioconductor.org) | [![ropensci_footer](http://ropensci.org/public_images/github_footer.png)](http://ropensci.org) |
|:-------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------:|