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etetoolkit
475 Stars 157 Forks GNU General Public License v3.0 2.5K Commits 123 Opened issues

Description

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.

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Overview

ETE (Environment for Tree Exploration) is a Python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. Clustering trees or any other tree-like data structure are also supported.

Given that ETE is mainly developed as a tool for researchers working in phylogenetics and genomics, it also provides specialized tools in that context (e.g. reconstructing, comparing and visualizing phylogenetic trees). If you use ETE in a published work, 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

Install and Documentation

  • The official web site of ETE is http://etetoolkit.org. Downloading instructions and further documentation can be found there.

  • News and announcements are usually posted on twitter: http://twitter.com/etetoolkit

Gallery of examples

.. image:: https://raw.githubusercontent.com/jhcepas/ete/master/sdoc/gallery.png :width: 600

Getting Support

Please, whenerver possible, avoid sending direct support-related emails to the developers. Keep communication public:

  • For any type of question on how to use ETE in the bioinformatics context, use BioStars (http://biostars.org) or even StackOverflow forums.

Please use the "etetoolkit" tag for your questions:

.. image:: http://img.shields.io/badge/stackoverflow-etetoolkit-blue.svg :target: https://stackoverflow.com/questions/tagged/etetoolkit+or+ete3

.. image:: http://img.shields.io/badge/biostars-etetoolkit-purple.svg :target: https://www.biostars.org/t/etetoolkit,ete3,ete,ete2/

  • Bug reports, feature requests and general discussion should be posted into github: 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 and account is validated.

  • For any other inquire (collaborations, sponsoring, etc), please contact jhcepas /at/ gmail.com

Contributing and BUG reporting

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

ROADMAP

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

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