Overview
ETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees. It is mainly written in Python, and includes many extra functionalities for phylogenetic trees.
Its main features include:
- Read and write support for trees in Newick format
- Multiple functions for traversing, searching and manipulating tree topologies and node annotations
- Integration with NCBI Taxonomic database
- Integration with GTDB database
- Programmatic visualization framework
- Visualization of huge trees based on adaptive zooming
- Comparing trees
- Phylogenetic functions
- orthology detection
- phylogenetic distance
- Command line tools
- phylogenetic reconstruction protocols
- tree comparison
- tree diff
The official website of ETE is http://etetoolkit.org. You can find downloading instructions and further documentation there.
News and announcements are usually posted on twitter: http://twitter.com/etetoolkit
If you use ETE, please cite:
Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
10.1093/molbev/msw046
Installation
Quick way
pip install https://github.com/etetoolkit/ete/archive/ete4.zip
For local development
To install ETE in a local directory to help with the development, you can:
- Clone this repository (
git clone https://github.com/etetoolkit/ete.git
) - Install dependecies
- If you are using conda:
conda install -c conda-forge cython bottle brotli numpy pyqt
- Otherwise, you can install them with
pip install <dependencies>
- If you are using conda:
- Build and install ete4 from the repository's root directory:
pip install -e .
Exploring a tree
To simply load a tree and start exploring it interactively, you can start a python session and write:
from ete4 import Tree
t = Tree(open(file_with_newick))
t.explore()
It will open a browser window with an interface to explore the tree.
Gallery of examples
Getting support
Rather than sending direct support-related emails to the developers, it is better to keep the communication public.
For question on how to use ETE in the bioinformatics context, use
Biostars with the etetoolkit
tag, or stack
overflow.
For bug reports, feature requests and general discussion, use https://github.com/etetoolkit/ete/issues
For more technical problems, you can also use the official ETE mailing list at https://groups.google.com/d/forum/etetoolkit. To avoid spam, messages from new users are moderated. Expect some delay until your first message appears after your account is validated.
For any other inquiries (collaborations, sponsoring, etc), please contact [email protected].
Contributing and bug reporting
https://github.com/etetoolkit/ete/wiki/Contributing