treeio: Base classes and functions for phylogenetic tree input and output

‘treeio’ is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

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

:writing_hand: Authors

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

https://yulab-smu.top

If you use 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.

Installation

Get the released version from Bioconductor:

## 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:

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

Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

:houses: Package Affiliations

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