Overview
etetoolkit is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “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 evo…”. The project has 34k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/etetoolkit`.
What etetoolkit does
Use ETE 4 to work with an existing tree:
What’s inside
The SKILL.md for etetoolkit is organised into these sections:
- 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
Installation
Add etetoolkit to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/etetoolkitReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
etetoolkit is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 33,821 GitHub stars
- Actively maintained — repository updated in the last 90 days
Author
Topics
Frequently asked questions
- What does etetoolkit 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 etetoolkit?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/etetoolkit in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is etetoolkit free to use?
- Yes. etetoolkit is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does etetoolkit come from?
- etetoolkit ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 33,821 GitHub stars apply to that whole collection, not to this skill on its own.