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etetoolkit — Claude Code skill: phylogenetic tree analysis with ETE 4

Analyzes phylogenetic trees with the ETE 4 library: compares topologies, annotates nodes, detects gene duplications, queries NCBI and GTDB taxonomy, and renders publication figures.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -a claude-code
Open on GitHub

What etetoolkit does

The skill applies ETE 4.4.0 tools to trees already built by alignment and inference software. It reads Newick and Nexus formats, prunes branches while preserving pairwise distances, finds common ancestors, and calculates Robinson-Foulds distance between topologies. For gene trees, it detects duplication and speciation events using a custom naming function.

Requires Python 3.10+ and the ete4==4.4.0 package. Visualization works through two paths: SmartView with the ete4[render-sm] extra for PNG screenshots, or the Qt renderer ete4[treeview] for PDF and SVG; the Qt option needs Chrome or Chromium. If you start with raw sequences, run alignment (MAFFT) and tree inference (IQ-TREE 2, FastTree) first—the skill picks up after that.

Public taxonomy downloads from NCBI and GTDB require internet access and consume substantial disk space, worth checking before the first update.

What it helps with

  • compare two topologies and calculate normalized RF distance
  • prune a tree to selected species while preserving pairwise branch lengths
  • detect duplication and orthology events in a gene tree
  • annotate nodes with metadata and write NHX format
  • query TaxID by species name in a local NCBI database

Example prompts for the agent

  • Read the tree from `tree.nw` with parser=1, prune to the species list in `species.txt`, and save to `pruned.nw`
  • Compare topologies in `tree_a.nw` and `tree_b.nw`, print RF distance and common leaves
  • Find duplications in `gene_tree.nw` where the prefix before `|` is the species code

How to install etetoolkit

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -a claude-code

2Manually: put the files in place

~/.claude/skills/etetoolkit/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/etetoolkit/

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Questions about etetoolkit

How to install etetoolkit in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -a claude-code. The skill will appear in ~/.claude/skills/etetoolkit/SKILL.md.

What does etetoolkit do?

It analyzes phylogenetic trees already built: compares topologies, prunes branches, detects gene duplication events, queries NCBI and GTDB taxonomy, and renders trees to PNG, PDF, or SVG.

Can etetoolkit build a tree from sequences?

No, the skill works with trees already constructed. For raw sequences, run alignment (MAFFT) and phylogenetic inference (IQ-TREE 2, FastTree) first, then load the result into ETE 4.

See also

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