Etetoolkit
If you're working with phylogenetic trees or doing any serious evolutionary analysis, this gives Claude direct access to the ETE toolkit. It handles the full workflow: reading Newick and NHX formats, detecting duplication and speciation events, identifying orthologs and paralogs, and rendering publication-quality visualizations as PDF or SVG. The NCBI taxonomy integration is genuinely useful for annotating trees with lineage information. The included command-line scripts for tree operations and visualization mean you can get results without writing Python every time. It's GPL-licensed, so factor that into your project's compliance requirements.
- skills.sh installs
- 2K
- GitHub stars
- 56.6K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add k-dense-ai/scientific-agent-skills --skill etetoolkit --agent claude-codeInstalls into .claude/skills of the current project.
Files
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 September 30, 2026.
Core, phylogeny, local synthetic taxonomy and helper checks target this released
package, not unreleased upstream changes. See
references/review.md for executed coverage and limitations.
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- Repository
- github.com/k-dense-ai/scientific-agent-skills
- Category
- AI & Agent Building
- First seen
- Jun 3, 2026
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