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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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:

Install and Documentation

Gallery of examples

Getting Support

Whenerver possible, please avoid sending support related emails directly to the developers. Keep communication public:

  • For any type of question on how to use ETE in a bioinformatics context, the BioStars community ( provides an excellent help desk. ETE developers contribute there with answers, but you will also get feedback from other users. It is recommended to tag your questions with the "etetoolkit" label.
  • For technical problems or more ETE specific questions, you can also use the official ETE mailing list at To avoid spam, messages from new users are moderated. Expect some delay until your first message and account is validated.
  • Bug reports, feature requests and general discussion should be posted into github:
  • For any other inquire please contact huerta /at/

Contributing and BUG reporting