A Python Environment for (phylogenetic) Tree Exploration

Welcome! This is the documentation for ETE 2.3.6, last updated Aug 11, 2015.

ETE is a Python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It provides a wide range of tree handling options, node annotation features and specialized features to deal with phylogenetic trees (i.e automatic orthology and paralogy detection, phylostratigraphy, tree reconciliation, etc). ETE implements also an interactive tree visualization system based on a a highly customizable tree drawing engine (PDF and SVG tree images). Although ETE is developed as a tool for phylogenetic analysis, it is also used to handle other types of hierarchical trees (i.e. clustering results).

API Tutorial How to use the different modules of the library Command line tools Tools to visualize, compare, and handle trees API Reference An index of all ETE functions

What's new in ETE 2.3? Previous versions Setup and Install ETE install and requirements Development Feature requests, bug reports, etc.

If you use ETE to analyze, process or visuallize results in a published work, please do not forget to support the project by citing:

Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24. doi:10.1186/1471-2105-11-24

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The official ETE web site is http://etetoolkit.org