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.

Core Capabilities

1. Tree Manipulation and Analysis

Load, manipulate, and analyze hierarchical tree structures with support for:

• Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
• Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
• Topology modification: Prune, root, collapse nodes, resolve polytomies
• Distance calculations: Compute branch lengths and topological distances between nodes
• Tree comparison: Calculate Robinson-Foulds distances and identify topological differences

Common patterns: