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ETE Toolkit 4 Tree Analysis

Analyze, compare, annotate and visualize phylogenetic and hierarchical trees with ETE 4

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
9 files

What it does

Teaches the agent how to work with existing phylogenetic (evolutionary family) trees using the ETE 4 Python library. Once installed, the agent can read Newick/Nexus tree files, prune, root and annotate them, compare two trees with Robinson-Foulds distances, detect duplication and speciation events in gene trees, look up NCBI or GTDB taxonomy, and render figures or open interactive views. It does not infer trees from raw sequences; that needs separate alignment and inference tools.

Great for

  • Biologists or bioinformaticians who already have a tree file and need to clean, compare or plot it
  • Students learning phylogenetics who want help with tree operations in Python
  • Developers porting older ETE 3 code to ETE 4

Skip it if

  • Building a tree from raw DNA or protein sequences, since it does not perform alignment or tree inference (use MAFFT, IQ-TREE or similar)
  • Clinical or legal conclusions about orthology or ancestry, because species-overlap calls are inferences from the supplied topology and naming function

Try asking

  • “Root this Newick tree at the midpoint, prune it to my 12 species and export it with host annotations”
  • “Compare these two trees with Robinson-Foulds distance and explain the differences”
  • “Detect duplication and speciation events in my gene tree using a species naming function”
  • “Look up NCBI taxonomy IDs for these species names and build a lineage summary”
Step-by-step guide: how to use ETE Toolkit 4 Tree AnalysisInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 9 original files, the MIT licence and an attribution note.

    etetoolkit.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip etetoolkit.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip etetoolkit.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Specify the Newick parser explicitly, since parser mismatches are the most common cause of errors and lost labels
  • Use the bundled scripts with validated inputs and review the taxonomy download size before the first update
  • Provide a curated species tree and unique leaf names when running reconciliation or Robinson-Foulds comparisons

What's inside

  • references/api_reference.md
  • references/migration-ete3-to-ete4.md
  • references/review.md
  • references/taxonomy.md
  • references/visualization.md
  • references/workflows.md
  • scripts/quick_visualize.py
  • scripts/tree_operations.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.