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.
npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 ETE does not replace sequence alignment or phylogenetic inference software. For raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or another inference tool; then load the resulting tree into ETE. ## Current Target This skill targets **ETE 4.4.0**, released September 3, 2025 and verified as the current PyPI release on July 23, 2026. Use `https://etetoolkit.github.io/ete/` for ETE 4 documentation. The `etetoolkit.org/docs/latest` pages are legacy ETE 3 documentation despite the URL name. Do not silently translate these examples back to ETE 3: - Package and import: `ete4`, not `ete3` - File input: pass an open file object; use strings for Newick text and do not rely on path-string heuristics
- Scope
- Current Target
- Installation
- Quick Start
- Core Workflows
- Inspect and transform a tree
- Compare two topologies
- Detect duplication and speciation events
- Query taxonomy
- Visualize
- Bundled Scripts
- Tree operations
- Visualization
- Quality and Interpretation Checks
uv pip install "ete4==4.4.0" SmartView static PNG screenshots uv pip install "ete4[render-sm]==4.4.0" Legacy Qt renderer for PNG, PDF, and SVG uv pip install "ete4[treeview]==4.4.0" uv run --with "ete4==4.4.0" python -c "import ete4; print(ete4.__version__)" uv run --with "ete4==4.4.0" python scripts/tree_operations.py \ stats tree.nw --parser 1 ascii tree.nw --parser 1 --props name,dist convert tree.nw output.nw \
What does the etetoolkit skill do?
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.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.