What problem does it solve?
ETE Toolkit streamlines phylogenetic tree manipulation, evolutionary event analysis, taxonomy annotation, and high-quality visualization so you can move from raw Newick files to publication-ready figures without stitching together many tools.
Core Features & Use Cases
- Tree manipulation & analysis: Load/write Newick and related formats, traverse, prune, reroot (including midpoint), compute distances, and compare topologies with Robinson–Foulds metrics.
- Phylogenetic event detection: Analyze gene trees to detect duplication/speciation events, support orthology/paralogy inference, and reconcile gene trees against species trees.
- NCBI taxonomy integration: Build lineage-aware views by translating between scientific names and TaxIDs, retrieving lineages, and annotating trees with taxonomic metadata.
- Publication-quality visualization: Render rectangular or circular trees to PDF/SVG/PNG with custom node styling and faces (including support-based coloring and advanced annotations).
- Clustering analysis: Use ClusterTree with linked matrices to evaluate clustering quality (e.g., silhouette and Dunn index) and visualize results.
Quick Start
Use ETE Toolkit to render a publication-quality visualization by applying the quick tree visualization script to your Newick tree file.
