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.
Python Perl6 Other

README.rst

README

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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.

ETE is currently developed as a tool for researchers working in phylogenetics and genomics. ETE provides specialized tools to reconstruct, compare and visualize phylogenetic trees. If you use ETE for 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/Documentation

Gallery of examples

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

Contributing and BUG reporting

https://github.com/jhcepas/ete/blob/master/CONTRIBUTING.rst

Getting support

  • There is a mailing list providing user support at https://groups.google.com/d/forum/etetoolkit. In order to avoid spam, messages from new users are moderated. Expect some delay until your first message and account is validated.
  • For general questions on how to use ETE in bioinformatic projects, the BioStars community (http://biostars.org) provides an excellent and broader help desk. Please feel free to raise any question there and tag it with the "etetoolkit" label.