etetoolkit

Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.

Quality

92%

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Passed

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Quality

Content

92%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.

A dense, executable, well-organized skill body that relies on one-level-deep references for detail and includes explicit validation checklists for risky operations. The only slight inefficiency is non-essential length in the citation section and version/date targeting.

Dimension	Reasoning	Score
Conciseness	The body is lean and assumes Claude's competence with no concept padding, but contains minor trimmable elements such as the lengthy citation block and version/date specifics that are not placed in a deprecated/old-patterns section, keeping it just below the leanest anchor.	4 / 5
Actionability	Provides fully executable, copy-paste-ready Python in Quick Start and every Core Workflow, plus concrete pinned 'uv run --with' bash commands for both bundled scripts, covering the common cases without pseudocode.	5 / 5
Workflow Clarity	Each workflow is clearly sequenced, with an explicit 7-item 'Quality and Interpretation Checks' checklist and concrete validation behavior (scripts refuse ambiguous/missing names; code raises on unresolved taxonomy names) serving as feedback checkpoints.	5 / 5
Progressive Disclosure	SKILL.md is a well-structured overview with a 'Reference Map' of one-level-deep links to five verified reference files and two scripts, and explicit 'Load only the reference needed for the task' guidance, making navigation easy.	5 / 5
	Total	19 / 20 Passed

Description

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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 highly specific, third-person description that clearly states capabilities, usage triggers, and an out-of-scope boundary, leaving little ambiguity about when to invoke it. The only gap is the absence of common tree-file extensions among the trigger terms.

Dimension	Reasoning	Score
Specificity	Lists many concrete actions (analyze, manipulate, compare, annotate, visualize) across named capabilities (Newick/Nexus I/O, topology edits/pattern matching, Robinson-Foulds, gene-tree reconciliation, NCBI/GTDB taxonomy, SmartView, publication rendering), giving comprehensive coverage rather than vague abstraction.	5 / 5
Completeness	Explicitly answers both 'what' (the action/capability list) and 'when' ('Use for…' trigger list), and adds a negative boundary ('Do not use it to infer trees from raw sequences'), matching the anchor for explicit what-and-when with concrete triggers.	5 / 5
Trigger Term Quality	Strong natural domain keywords (phylogenetic/hierarchical trees, Newick/Nexus, Robinson-Foulds, gene trees, NCBI/GTDB, SmartView), but missing common file extensions such as .nwk/.nex/.tre that a user might naturally mention, so it sits just below the comprehensive anchor.	4 / 5
Distinctiveness Conflict Risk	Occupies a clear niche (ETE 4 phylogenetic/hierarchical tree work) with distinct, domain-specific triggers and an explicit out-of-scope statement that minimizes overlap with sequence-alignment or inference skills.	5 / 5
	Total	19 / 20 Passed

Validation

100%

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 — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/etetoolkit/SKILL.md
Commit: 1e5eeff

Reviewed: 4 days ago

Table of Contents

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