treeio: Base classes and functions for phylogenetic tree input and output
βtreeioβ 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.
βοΈ Authors
Guangchuang YU
School of Basic Medical Sciences, Southern Medical University
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.
β¬ 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("GuangchuangYu/treeio")
π Contributing
We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.
ποΈ Package Affiliations
The treeio
package is a part of the Bioconductor and rOpenSci
projects.