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Agent skill

Etetoolkit

by aipoch in aipoch/medical-research-skills

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…

MITAuto-check passedData & Analytics

Install Etetoolkit

skills CLI
$ npx skills add aipoch/medical-research-skills --skill etetoolkit -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills etetoolkit --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Data Analysis/etetoolkit' .claude/skills/etetoolkit && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
etetoolkit
GitHub stars
2k
Token cost
~1.4k tokens
SKILL.md length
459 words
Files
7 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…

  • Works in 4 steps: Load a gene tree (optionally with an… → Provide a species naming function to map… → Run descendant event detection. → …
  • You need to parse/manipulate Newick/NHX trees
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder

What it does

Etetoolkit is an agent skill from aipoch/medical-research-skills. ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 8 other files, including scripts and reference files (for example `etetoolkit_audit_result_v1.json`, `references/api_reference.md` and `references/visualization.md`).

It sits in Data & Analytics, covering Bioinformatics and Data visualization. It works with NCBI. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need to parse/manipulate Newick/NHX trees
  • Detect duplication/speciation events
  • Integrate NCBI taxonomy
  • Render publication-quality figures

Example prompts

  • “/etetoolkit”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Load a gene tree (optionally with an alignment).
  2. Provide a species naming function to map gene IDs → species.
  3. Run descendant event detection.
  4. Extract ortholog groups (speciation subtrees) or query ortholog/paralog sets from events.

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 2 files in scripts/ (Python), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Etetoolkit loads about 1.4k tokens when it runs, and up to ~15k if it reads all its reference files. Until then it costs about 67 tokens; SKILL.md has 459 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~67
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~15k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 459 words, ~1,433 tokens.

Download SKILL.mdSave it as .claude/skills/etetoolkit/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.
name
etetoolkit
description
ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • Preprocess phylogenetic trees: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses.
  • Detect evolutionary events in gene trees: infer duplication vs. speciation events and derive ortholog/paralog relationships for phylogenomics.
  • Annotate trees with taxonomy: map species names to NCBI TaxIDs, retrieve lineages/ranks, and build minimal taxonomy topologies connecting a set of taxa.
  • Generate publication-quality visualizations: render trees to PDF/SVG/PNG with custom styles, support-based coloring, and node “faces” (labels, shapes, heatmaps).
  • Compare alternative topologies: quantify differences between trees using Robinson–Foulds (RF) distance and partition/bipartition analysis.

Key Features

  • Tree I/O and manipulation
    • Read/write: Newick, NHX, PhyloXML, NeXML
    • Traversals: preorder, postorder, levelorder
    • Operations: prune, reroot, collapse, resolve polytomies
    • Metrics: branch/topological distances, RF distance
  • Phylogenetic (gene tree) analysis
    • Alignment association (FASTA/Phylip)
    • Species name extraction from gene IDs
    • Duplication/speciation detection (e.g., species overlap / reconciliation-style workflows)
    • Orthology/paralogy extraction and gene-family splitting
  • NCBI taxonomy integration
    • Auto-download + local cache of taxonomy DB
    • TaxID ↔ scientific name translation
    • Lineage/rank retrieval and taxonomy-based topology building
    • Tree annotation with taxonomic metadata
  • Visualization
    • Rectangular/circular layouts, GUI exploration
    • NodeStyle/TreeStyle customization
    • Faces (text, shapes, charts/heatmaps) and layout functions
    • Export to PDF/SVG/PNG
  • Clustering support
    • ClusterTree for dendrograms linked to numeric matrices
    • Cluster quality metrics (e.g., silhouette, Dunn index)
    • Heatmap + tree combined views

Dependencies

  • ete3 (recommended: >=3.1.0)
  • Optional GUI/rendering dependencies (platform-specific):
    • PyQt5 (e.g., >=5.15)
    • Qt SVG support (often packaged as python3-pyqt5.qtsvg on Debian/Ubuntu)

Example Usage

The following example is designed to be runnable end-to-end (it uses an in-memory Newick string and does not require external files).

python
# pip install ete3

from ete3 import Tree, TreeStyle, NodeStyle

# 1) Load a tree (Newick)
nw = "((A:0.1,B:0.2)90:0.3,(C:0.2,D:0.4)70:0.1);"
t = Tree(nw, format=1)

# 2) Basic stats
print("Leaves:", len(t))
print("Total nodes:", sum(1 for _ in t.traverse()))

# 3) Midpoint rooting
mid = t.get_midpoint_outgroup()
t.set_outgroup(mid)

# 4) Prune to taxa of interest (preserve branch lengths)
t.prune(["A", "C", "D"], preserve_branch_length=True)

# 5) Style nodes (color internal nodes by support)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_support = True

for n in t.traverse():
    st = NodeStyle()
    if n.is_leaf():
        st["fgcolor"] = "blue"
        st["size"] = 8
    else:
        # ETE stores internal support in n.support when present
        st["fgcolor"] = "darkgreen" if getattr(n, "support", 0) >= 80 else "red"
        st["size"] = 5
    n.set_style(st)

# 6) Render (PDF/SVG/PNG supported depending on your environment)
t.render("example_tree.pdf", tree_style=ts)
print("Wrote: example_tree.pdf")

Implementation Details

Show full SKILL.md (210 more words)Show less
Tree parsing formats (Newick “format” codes)

ETE uses a format integer to control how node attributes are interpreted when reading/writing Newick. Common patterns:

  • format=0: flexible default (often includes branch lengths)
  • format=1: includes internal node names
  • format=2: includes support/bootstrap values
  • format=5: internal node names + branch lengths
  • format=8: name + distance + support (maximal common usage)
  • format=9: leaf names only
  • format=100: topology only

Example:

python
from ete3 import Tree

t = Tree("tree.nw", format=1)
t.write(outfile="out.nw", format=5)
NHX feature preservation

NHX is used to store custom per-node features. When writing, specify which features to serialize:

python
t.write(outfile="tree.nhx", features=["taxid", "habitat", "lineage"])
Rerooting and pruning behavior
  • Midpoint rooting uses get_midpoint_outgroup() to select an outgroup that balances path lengths.
  • Pruning should typically use preserve_branch_length=True to avoid distorting distances in phylogenetic contexts.
Evolutionary event detection (gene trees)

For gene trees, PhyloTree supports event labeling on internal nodes (commonly:

  • evoltype == "D" for duplication
  • evoltype == "S" for speciation)

A typical workflow is:

  1. Load a gene tree (optionally with an alignment).
  2. Provide a species naming function to map gene IDs → species.
  3. Run descendant event detection.
  4. Extract ortholog groups (speciation subtrees) or query ortholog/paralog sets from events.
Tree comparison (Robinson–Foulds)

Tree.robinson_foulds(other_tree) returns:

  • rf: RF distance (number of differing bipartitions)
  • max_rf: maximum possible RF given shared leaves
  • plus shared leaves and partition sets for deeper inspection

Normalized RF is typically computed as rf / max_rf (when max_rf > 0).

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files (scripts, references) in scientific-skills/Data Analysis/etetoolkit of aipoch/medical-research-skills.

  • SKILL.md
  • etetoolkit_audit_result_v1.json
  • references/api_reference.md
  • references/visualization.md
  • references/workflows.md
  • scripts/quick_visualize.py
  • scripts/tree_operations.py

Open the folder on GitHubat commit 686e09d

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Works with

Categories

Questions about Etetoolkit

What does Etetoolkit do?

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events…. Etetoolkit is an agent skill from aipoch/medical-research-skills. ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

When should I use Etetoolkit?

Etetoolkit fits situations like: you need to parse/manipulate Newick/NHX trees; detect duplication/speciation events; integrate NCBI taxonomy; render publication-quality figures.

How do I install Etetoolkit in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill etetoolkit -a claude-code`. Or copy the skill folder (scientific-skills/Data Analysis/etetoolkit in aipoch/medical-research-skills) into .claude/skills/etetoolkit in your project. Claude Code loads it when a task matches its description.

How do I install Etetoolkit in Codex?

Run `npx skills add aipoch/medical-research-skills --skill etetoolkit -a codex`. Or copy the skill folder (scientific-skills/Data Analysis/etetoolkit in aipoch/medical-research-skills) into .agents/skills/etetoolkit in your project. Codex loads it when a task matches its description.

Can I use Etetoolkit in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill etetoolkit -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/etetoolkit, .gemini/skills/etetoolkit, .github/skills/etetoolkit and .opencode/skills/etetoolkit in your project.

What does Etetoolkit need to run?

Going by SKILL.md and its folder, Etetoolkit needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Etetoolkit access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Etetoolkit safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Etetoolkit use?

Etetoolkit is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Etetoolkit use?

About 1.4k tokens (SKILL.md is roughly 5.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 14k tokens, read only when the agent opens those files.

What are the alternatives to Etetoolkit?

Skills that share tags, products or a category with Etetoolkit: Bioconductor Biomart (bioMate-AI/biomate-bioconductor-kb, 804 stars), Bio Data Visualization Dimensionality Reduction Plots (GPTomics/bioSkills, 1.2k stars), Bio Data Visualization Manhattan Qq Locuszoom (GPTomics/bioSkills, 1.2k stars) and Bio Sashimi Plots (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Etetoolkit?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.