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.

When to Use

• Parsing, traversing, or reformatting tree files (Newick / NHX / PhyloXML / NeXML)
• Pruning, rooting, collapsing, or resolving polytomies in a tree
• Detecting duplication/speciation events and inferring orthologs/paralogs from gene trees
• Querying NCBI Taxonomy (taxid/name translation, lineages, taxonomy trees)
• Producing publication-quality PDF/SVG/PNG tree figures
• Comparing trees (Robinson-Foulds) or analyzing clustering dendrograms

Core Capabilities