Individual skill
etetoolkit
Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.
skills/etetoolkit/SKILL.md
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- Last checked
- Nov 10, 2026
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- Repository last updated
- Nov 9, 2026
- License
- MIT
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- ai-scientist Repository topic
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# ETE Toolkit 4
## Scope
Use ETE 4 to work with an existing tree:
- Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write
Newick trees
- Compare topologies and calculate phylogenetic distances
- Find repeated subtree topologies with `TreePattern`
- Analyze gene trees with `PhyloTree`
- Query local NCBI or GTDB taxonomy databases
- Explore large trees interactively with SmartView
- Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview