Individual skill
etetoolkit
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for 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. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.
plugins/KalarisLabs/research-agent-skills/skills/etetoolkit/SKILL.md
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- Last checked
- Nov 4, 2026
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- Nov 6, 2026
- License
- Apache-2.0
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Read excerpt
# 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