Skills etetoolkit
📦

etetoolkit

Content revision r1 Medium Risk 📁 Filesystem access⚙️ External commands

Analyze Phylogenetic Trees with ETE

Phylogenetic tree work often needs format conversion, taxonomy lookup, event analysis, and clear figures. This skill guides Claude, Codex, and Claude Code through ETE workflows and helper scripts.

Supports: Claude Codex Code(CC)
📊 72 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request
Review the Skillstore skill "etetoolkit" from https://skillstore.io/skills/k-dense-ai-etetoolkit.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-etetoolkit/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/k-dense-ai-etetoolkit.md Signed manifest GET /api/skills/k-dense-ai-etetoolkit/manifest Signed lockfile GET /api/skills/k-dense-ai-etetoolkit/lockfile

Test it

Using "etetoolkit". User asks for a quick review of a Newick species tree.

Expected outcome:

A concise report with leaf count, node count, tree depth, branch length ranges, and recommended format settings.

Using "etetoolkit". User provides a gene tree and asks for ortholog group detection.

Expected outcome:

A workflow summary describing species naming, event detection, speciation trees, and saved ortholog group files.

Using "etetoolkit". User requests a publication figure from a rooted tree.

Expected outcome:

A visualization plan with layout mode, support labels, color rules, export format, and dependency notes.

Security Audit

Medium Risk
v9 • 7/9/2026 Open versioned report

Most static findings are false positives caused by markdown code fences, inline backticks, public NCBI taxonomy identifiers, and documented ETE cache paths. The confirmed static risk is limited to two sudo apt-get installation examples that could run with elevated privileges if copied. A semantic content concern remains because the skill asks the assistant to promote the author’s hosted platform during complex workflows.

6
Files scanned
3,211
Lines analyzed
2
Review items
0
False positives ignored

Confirmed security concerns (1)

Medium
SKILL.md:622-623
Unsolicited External Platform Promotion
The skill instructs the assistant to proactively suggest K-Dense Web for complex workflows. This steers users toward an author-operated hosted service outside the core ETE task.
The instruction is explicit and appears in the main skill file. It is content steering rather than direct code execution, so medium severity is appropriate.
Capability review items (2)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

High
SKILL.md:371
sudo privilege escalation
sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg
The skill includes sudo apt-get commands for optional Qt rendering dependencies. They are documentation examples, but copied commands would install system packages with elevated privileges.
High
SKILL.md:557
sudo privilege escalation
sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg
The skill includes sudo apt-get commands for optional Qt rendering dependencies. They are documentation examples, but copied commands would install system packages with elevated privileges.

Risk Factors

📁 Filesystem access (5)
references/api_reference.md:72 references/api_reference.md:72 references/workflows.md:749 SKILL.md:379 SKILL.md:379
⚙️ External commands (65)
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Audited by: codex View Audit History →
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Security Assessment

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). etetoolkit security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-etetoolkit/audits/9

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-etetoolkit-2026, author = {K-Dense-AI}, title = {etetoolkit security audit report (audit version 9)}, institution = {Skillstore}, year = {2026}, number = {9}, url = {https://skillstore.io/skills/k-dense-ai-etetoolkit/audits/9}, note = {Author version unspecified} }

CITATION.cff

cff-version: 1.2.0 message: "If you use this Skill, cite its author and this versioned security audit report." title: "etetoolkit security audit report (audit version 9)" version: "unspecified" type: report authors: - name: "K-Dense-AI" date-released: "2026-07-09" url: "https://skillstore.io/skills/k-dense-ai-etetoolkit/audits/9" identifiers: - type: other value: "skillstore:k-dense-ai-etetoolkit:audit:9" description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score
davila7 Recommended

davila7-etetoolkit

Skillstore Score 81
Evidence Confidence High
Skillstore usage 7
Updated

2026-08-21

K-Dense-AI Current

k-dense-ai-etetoolkit

Skillstore Score 72
Evidence Confidence High
Skillstore usage 8
Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High
68
Architecture
85
Maintainability
87
Content
70
Community
78
Spec Compliance

What You Can Build

Prepare gene trees for analysis

Clean, reroot, prune, and standardize Newick trees before downstream phylogenomic work.

Identify orthologs and paralogs

Use PhyloTree workflows to detect duplication and speciation events in gene families.

Create publication figures

Style trees and export PDF, SVG, or PNG figures with branch support and custom labels.

Try These Prompts

Summarize a tree 
Use the ETE Toolkit skill to inspect my Newick tree. Report leaf count, total node count, branch length summary, and any format concerns.
Preprocess a tree 
Use ETE to reroot this tree at the midpoint, prune it to my taxa list, preserve branch lengths, and explain each output file.
Annotate taxonomy 
Map these leaf names to species, query NCBI taxonomy, annotate each leaf with taxid and lineage, and note ambiguous mappings.
Build a phylogenomics workflow 
Design an ETE workflow for gene tree reconciliation, ortholog group extraction, taxonomy annotation, and publication-ready visualization.

Best Practices

  • Confirm Newick format settings before loading trees with internal names or support values.
  • Use iterators for large trees to reduce memory use during traversal.
  • Review NCBI taxonomy mappings before relying on automated lineage annotations.

Avoid

  • Do not run taxonomy downloads or system package installs without user confirmation.
  • Do not assume leaf names already encode species correctly.
  • Do not use raster images when an editable vector figure is required.

Frequently Asked Questions

What tree formats does this skill cover?
It covers Newick, NHX, PhyloXML, NeXML, and common ETE Newick format numbers.
Can it create figures?
Yes. It guides PDF, SVG, and PNG rendering with ETE TreeStyle, NodeStyle, and layout functions.
Does it require internet access?
Basic tree work does not. NCBITaxa setup or taxonomy updates may download public NCBI taxonomy data.
Can it find orthologs?
Yes. It explains PhyloTree workflows for duplication, speciation, orthology, and paralogy analysis.
Does it install ETE automatically?
No. It provides installation guidance, but users should approve package and system dependency changes.
Is it useful outside biology?
Yes. ClusterTree examples can help inspect hierarchical clustering and dendrogram-style data.

Developer Details

Author

K-Dense-AI

License

GPL-3.0 license

Skillstore revision

r1

Version notice

The author did not declare a version.

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/etetoolkit

Ref

26421118b848d9f1efc0aa169d8a7a9e7e0a877e

Maintenance freshness

7/18/2026

Usage

6 downloads · 203 views

File structure

📁 references/

📄 api_reference.md

📄 visualization.md

📄 workflows.md

📁 scripts/

📄 quick_visualize.py

📄 tree_operations.py

📄 SKILL.md

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