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https://github.com/etetoolkit/ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
https://github.com/etetoolkit/ete
phylogenetics phylogenomic python tree-structure treeview visualization
Last synced: 3 months ago
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Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
- Host: GitHub
- URL: https://github.com/etetoolkit/ete
- Owner: etetoolkit
- License: gpl-3.0
- Created: 2010-11-13T16:04:25.000Z (about 14 years ago)
- Default Branch: ete4
- Last Pushed: 2024-10-28T18:02:07.000Z (3 months ago)
- Last Synced: 2024-10-28T18:58:15.886Z (3 months ago)
- Topics: phylogenetics, phylogenomic, python, tree-structure, treeview, visualization
- Language: Python
- Homepage: http://etetoolkit.org
- Size: 125 MB
- Stars: 790
- Watchers: 34
- Forks: 214
- Open Issues: 226
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
[](https://travis-ci.org/etetoolkit/ete)
[](https://gitter.im/jhcepas/ete?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete4)
[](https://www.biostars.org/t/etetoolkit,ete,ete2,ete3,ete4/)
[](CODE_OF_CONDUCT.md)
# 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
```sh
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](https://conda.io/):
`conda install -c conda-forge cython bottle brotli numpy scipy`
- Otherwise, you can install them with `pip install `
- Build and install ete4 from the repository's root directory: `pip install -e .`
## Optional dependencies
If you want to use the `treeview` module (which depends on
[PyQt](https://www.riverbankcomputing.com/software/pyqt/)), you can
add `[treeview]` to the pip installation.
For example with `pip install -e .[treeview]` for a local editable
installation. Or `pip install -e .[treeview,test,doc]` to also include
the modules for testing and generating the documentation.
# Exploring a tree
To simply load a tree from a file (`my_tree.nw`) and start exploring
it interactively, you can use the `ete4` utility and run:
```sh
ete4 explore -t my_tree.nw
```
Or start a python session and write:
```py
from ete4 import Tree
t = Tree(open('my_tree.nw'))
t.explore()
```
It will open a browser window with an interface to explore the tree.
# Documentation
Most documentation is automatically generated with
[sphinx](https://www.sphinx-doc.org) from the contents of the `doc`
directory, and is available at https://etetoolkit.github.io/ete/ .
# 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](http://biostars.org) with the `etetoolkit` tag, or [stack
overflow](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete4).
[](https://www.biostars.org/post/search/?query=etetoolkit+or+ete+or+ete2+or+ete3+or+ete4)
[](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete3+or+ete4)
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].
# Tests
You can launch some tests by running:
```sh
./run_tests.py
```
# Contributing and bug reporting
https://github.com/etetoolkit/ete/wiki/Contributing
# Roadmap
https://github.com/etetoolkit/ete/wiki/ROADMAP