etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Quality

73%

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Securityby

Passed

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tessl review fix ./bundled/skills/etetoolkit/SKILL.md

Quality

Content

65%

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

The skill is highly actionable with verified executable code and scripts and well-signaled references, but it is over-long with redundant inline content and lacks validation/feedback checkpoints in its batch and destructive workflows.

Suggestions

Trim the 'Common Use Cases' section or fold it into 'Core Capabilities' to remove duplicated phylogenetic-analysis, visualization, and tree-manipulation content and cut the body toward a lean overview.

Push detailed visualization/workflow code into references/visualization.md and references/workflows.md, leaving SKILL.md as a concise overview with one-line pointers.

Add explicit validation/feedback steps to batch and destructive workflows — e.g. verify a re-rooted/pruned tree's leaf count before saving, and validate the NCBI taxonomy download succeeded before querying.

Dimension	Reasoning	Score
Conciseness	The body avoids concept-explaining fluff and is mostly code, but at ~600 lines it is padded with redundancy — the 'Common Use Cases' section re-covers phylogenetic analysis, visualization, and tree manipulation already detailed in 'Core Capabilities' — so it is not the lean, every-token-earns-its-place level 3.	2 / 3
Actionability	Provides fully executable Python snippets and concrete bash commands with real flags, and the referenced scripts (tree_operations.py, quick_visualize.py) are verified to exist, making the guidance copy-paste ready.	3 / 3
Workflow Clarity	Workflows like Use Case 1 (numbered 1–6) and Use Case 4 (batch tree processing) are sequenced, but none include validation checkpoints or validate→fix→retry feedback loops for destructive/batch operations, which caps workflow clarity at 2.	2 / 3
Progressive Disclosure	The Reference Documentation section clearly signals one-level-deep references (api_reference.md, workflows.md, visualization.md, all verified present), but the body duplicates extensive workflow and visualization code that already lives in those references, so content that should be separate is inline.	2 / 3
	Total	9 / 12 Passed

Description

82%

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

The description is specific, distinctive, and rich in natural trigger terms, but it omits an explicit 'Use when...' clause, leaving the 'when' only implied and capping completeness.

Suggestions

Append an explicit trigger clause, e.g. 'Use when working with phylogenetic trees, Newick/NHX files, orthology analysis, or NCBI taxonomy.' to satisfy the completeness 'when' requirement.

Add a couple of common user phrasings (e.g. 'phylogeny', 'evolutionary tree', 'tree of life') to broaden trigger coverage.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions — 'Tree manipulation (Newick/NHX)', 'evolutionary event detection', 'orthology/paralogy', 'NCBI taxonomy', 'visualization (PDF/SVG)' — matching the score-3 anchor of several distinct concrete actions, not the single-domain level 2.	3 / 3
Completeness	Clearly states what the skill does but lacks an explicit 'Use when...' trigger; the trailing 'for phylogenomics' is an implied domain tag, not trigger guidance, so per the missing-trigger cap it stays at 2 rather than 3.	2 / 3
Trigger Term Quality	Uses natural domain terms a user would actually say — 'phylogenetic tree', 'Newick/NHX', 'orthology/paralogy', 'NCBI taxonomy', 'phylogenomics' — giving good coverage rather than jargon-only or generic terms.	3 / 3
Distinctiveness Conflict Risk	The ETE/Newick/NHX/NCBI taxonomy niche is sharply scoped with distinct triggers, making it unlikely to fire for an unrelated skill.	3 / 3
	Total	11 / 12 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
skill_md_line_count	SKILL.md is long (618 lines); consider splitting into references/ and linking	Warning

	Total	15 / 16 Passed

Repository: foryourhealth111-pixel/Vibe-Skills
Path: bundled/skills/etetoolkit/SKILL.md
Commit: f627ab5

Reviewed: about 8 hours ago

Table of Contents

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