etetoolkit

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

Quality

68%

Does it follow best practices?

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Securityby

Passed

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

Quality

Content

61%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.

The body is highly actionable with executable code and CLI examples that align with the bundled scripts and references, and it is well structured for progressive disclosure. It is somewhat verbose for the context budget and lacks validation checkpoints in its batch/destructive workflows.

Suggestions

Add explicit validation checkpoints to batch/destructive workflows (e.g. after Use Case 4's node deletion, verify leaf count/topology before writing, and re-load the output to confirm it parses).

Trim boilerplate that Claude already knows — the generic 10-item Best Practices list and the troubleshooting/installation prose could be condensed or moved to a reference file.

Verify clustering API names (get_silhouette/get_dunn and tree.show("heatmap")) against actual ete3 signatures, and fix the 'Silhouette' typo, to keep the executable examples trustworthy.

Dimension	Reasoning	Score
Conciseness	The 617-line body is mostly efficient code-plus-bullets, but several sections pad tokens with concepts Claude already knows (generic best-practices list, an installation/troubleshooting section, explanatory intros like 'Load, manipulate, and analyze hierarchical tree structures with support for:'), so it could be tightened.	3 / 5
Actionability	Numerous copy-paste-ready Python blocks and exact CLI commands whose flags match the bundled scripts (e.g. tree_operations.py reroot --midpoint, prune --keep-taxa; quick_visualize.py --mode c --color-by-support), with only minor correctness concerns in clustering metric calls.	4 / 5
Workflow Clarity	Use cases lay out numbered pipelines, but batch/destructive operations (e.g. Use Case 4 deleting low-support nodes across many trees) lack explicit validation or verification checkpoints, which caps workflow clarity at 3 per the rubric.	3 / 5
Progressive Disclosure	Good one-level-deep structure: an overview plus six capability sections, a clearly signaled Reference Documentation section pointing to three real reference files, and two bundled scripts whose referenced paths all resolve; minor gaps remain where some API detail is still inlined rather than delegated.	4 / 5
	Total	14 / 20 Passed

Description

75%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.

The description is specific and distinctive, naming concrete capabilities and format keywords that signal the phylogenetics niche well. Its main weakness is the absence of an explicit 'Use when…' trigger clause, which caps completeness at 3.

Suggestions

Append an explicit trigger clause, e.g. 'Use when working with phylogenetic trees, Newick/NHX files, gene-tree orthology analysis, or NCBI taxonomy.'

Add a couple of natural synonyms users say (e.g. 'phylogeny', 'species tree', 'build a tree') to broaden trigger coverage.

Optionally mention input file extensions (e.g. .nw, .nwk, .nhx) alongside the format names.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions within a named domain — 'Tree manipulation (Newick/NHX)', 'evolutionary event detection', 'orthology/paralogy', 'NCBI taxonomy', 'visualization (PDF/SVG)' — giving comprehensive coverage rather than vague phrasing.	5 / 5
Completeness	The 'what' is clearly stated, but there is no 'Use when…' clause or equivalent explicit trigger guidance, so per the rubric completeness is capped at 3.	3 / 5
Trigger Term Quality	Good keyword coverage including natural domain terms and format names ('Newick/NHX', 'orthology/paralogy', 'NCBI taxonomy', 'PDF/SVG', 'phylogenomics'), but a few synonyms a user might naturally say ('phylogeny', 'build a species tree') and explicit extensions beyond the format names are absent.	4 / 5
Distinctiveness Conflict Risk	The description carves out a clear, specialized niche (ETE phylogenetic toolkit) with distinct triggers and minimal overlap risk with unrelated skills.	5 / 5
	Total	17 / 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
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: d5ae560

Reviewed: 1 day ago

Table of Contents

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