treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.

By Li-Gen Wang, T. T. Lam, Shuangbing Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, Casey W. Dunn, B. Jones, Tyler C. Bradley and 4 more. Molecular biology and evolution, 2019

543 citations recorded by the source corpus.

Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/aa3096401633a0aa078cf242a363cd42d811bfec

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecological Modeling

1. Li Zhan
2. Meijun Chen
3. Wenli Tang
4. Zehan Dai
5. Yi Guan
6. T. T. Lam
7. Shuangbin Xu
8. Xiao Luo

In Genetics

1. Guangchuang Yu
2. Li Zhan
3. Meijun Chen
4. Wenli Tang
5. Yi Guan
6. T. T. Lam

In Molecular Biology

1. Guangchuang Yu
2. Zehan Dai
3. Li Zhan
4. Meijun Chen
5. Wenli Tang
6. Yi Guan
7. Lin Li
8. Shuangbin Xu

Citations in the corpus

• Using ggtree to Visualize Data on Tree‐Like Structures (2020, methodology): “In the example below, a tree in New Hamp-shire eXtended (NHX) format was parsed into R using the treeio package (Wang et al., 2020).”
• Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data (2022, methodology): “The tree object can be further processed using the tidytree or treeio packages and can be exported to Newick, Nexus, or BEAST Nexus, which enables associated data to be stored as annotated elements [5].”
• ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data (2021, unknown): “Phylogenetic data imported by the treeio (Wang et al. 2020)”