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 and Nexus formats
• 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

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

There are several ways to install ETE.

Quick way

pip install ete4

will get you the latest release from PyPI.

… or with conda

conda install conda-forge::ete4

to get it from conda-forge.

… or using the very latest from the repository

pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip

if you want to be up-to-date with the very last commit done, even before release.

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 cheroot brotli numpy scipy
  • Otherwise, you can install them with pip install <dependencies>
• 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), 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,render_sm] to also include the modules for testing, generating the documentation, and smartview file rendering.

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:

ete4 explore -t my_tree.nw

Or start a python session and write:

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 from the contents of the doc directory, and is available at https://etetoolkit.github.io/ete/ .

Gallery of examples

There is an ETE Gallery with a tutorial, examples and course material to learn about the graphical capabilities of ETE.

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 jhcepas@gmail.com.

Tests

You can launch some tests by running:

./run_tests.py

To see all the available options for running the tests, use:

./run_tests.py -h

Contributing and bug reporting

https://github.com/etetoolkit/ete/wiki/Contributing