ETE Toolkit Skill

Overview

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.

ete3 or ete4?

The examples in this skill and its references are written for ete3 3.1.3, which is still what most published pipelines import — but ete3 has had no release since May 2023, and ete4 (4.4.0, Sept 2025) is the maintained line. Port deliberately: the ete4 API is not drop-in.