etetoolkit

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.

Quality

85%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide

Securityby

Passed

No findings from the security scan

Quality

Content

78%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

Actionable and well-sequenced content with a runnable example and useful implementation details, weakened mainly by unsignaled bundle files and minor redundancy between the 'When to Use' and 'Key Features' sections.

Suggestions

Add explicit pointers to the existing bundle files where relevant (e.g., under Visualization: 'See references/visualization.md'; under event detection / RF: 'See references/workflows.md'; for full method coverage: 'See references/api_reference.md'; runnable helpers: 'See scripts/quick_visualize.py and scripts/tree_operations.py').

Collapse the redundancy between 'When to Use' and 'Key Features' — keep one as trigger-oriented bullets and let the other link out to detail, instead of restating the same capability list twice.

Add a light verification checkpoint to the main workflow and the event-detection workflow (e.g., print/inspect the pruned tree or counts before rendering, confirm evoltype labels before extracting ortholog groups).

Dimension	Reasoning	Score
Conciseness	Mostly efficient with executable snippets and minimal concept re-explanation, but the 'When to Use' and 'Key Features' sections restate the same capabilities, creating mild redundancy that could be tightened.	4 / 5
Actionability	Provides a complete, copy-paste-ready, runnable end-to-end example (in-memory Newick through render) plus concrete snippets for format I/O, NHX features, and RF distance covering the common cases.	5 / 5
Workflow Clarity	The main example and the evolutionary-event-detection section are clearly sequenced with numbered steps, but verification checkpoints are implicit (e.g., no 'verify the tree/pruning result' step), leaving minor validation gaps.	4 / 5
Progressive Disclosure	The body is well-sectioned but never signals the provided bundle files (references/visualization.md, workflows.md, api_reference.md, scripts/*.py); deeper material exists yet navigation to it is absent, so references are present but not clearly signaled.	3 / 5
	Total	16 / 20 Passed

Description

92%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong, specific description that clearly states capabilities and an explicit 'use when' trigger covering concrete phylogenetic-tree tasks. Only minor weakness is the absence of file-extension synonyms in the trigger terms.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'parse/manipulate Newick/NHX trees', 'detect duplication/speciation events', 'integrate NCBI taxonomy', 'render publication-quality figures' — giving comprehensive coverage rather than vague domain naming.	5 / 5
Completeness	Explicitly states both what ('toolkit for phylogenetic and hierarchical tree analysis' with listed actions) and when ('use it when you need to...') with concrete trigger phrases.	5 / 5
Trigger Term Quality	Strong natural terms (phylogenetic trees, Newick/NHX, duplication/speciation, NCBI taxonomy, publication-quality figures) but omits common synonyms and file extensions (.nwk, .nhx, .tre) that users would mention.	4 / 5
Distinctiveness Conflict Risk	Names a specific toolkit (ETE) and niche (Newick/NHX, NCBI taxonomy, duplication/speciation detection) with distinct triggers, giving minimal overlap with other skills.	5 / 5
	Total	19 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/etetoolkit/SKILL.md
Commit: f5ef65b

Reviewed: ~2 hours ago

Table of Contents

Discovery Implementation Validation

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.