etetoolkit
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.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
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.
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 RiskMost 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.
Confirmed security concerns (1)
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.
Risk Factors
📁 Filesystem access (5)
⚙️ External commands (65)
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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/9BibTeX 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 variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-etetoolkit
2026-08-21
k-dense-ai-etetoolkit
2026-08-21
Skillstore Score
Why this score Evidence Confidence: HighWhat 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
Use the ETE Toolkit skill to inspect my Newick tree. Report leaf count, total node count, branch length summary, and any format concerns.
Use ETE to reroot this tree at the midpoint, prune it to my taxa list, preserve branch lengths, and explain each output file.
Map these leaf names to species, query NCBI taxonomy, annotate each leaf with taxid and lineage, and note ambiguous mappings.
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?
Can it create figures?
Does it require internet access?
Can it find orthologs?
Does it install ETE automatically?
Is it useful outside biology?
Developer Details
Author
K-Dense-AILicense
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/etetoolkitRef
26421118b848d9f1efc0aa169d8a7a9e7e0a877e
Maintenance freshness
7/18/2026
Usage
6 downloads · 203 views
File structure