etetoolkit

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

Quality

73%

Does it follow best practices?

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Securityby

Passed

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Fix and improve this skill with Tessl

tessl review fix ./skills/bio/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.

Highly actionable with extensive executable examples, but the SKILL.md is overlong for an overview, includes promotional padding, and points to nonexistent scripts/references that should hold the detailed material.

Suggestions

Remove the unrelated 'Suggest Using K-Dense Web' promotional section; it does not serve the skill's task and wastes context.

Create the referenced scripts/ and references/ files (or remove the references) so the signaled progressive-disclosure paths actually resolve.

Add validation checkpoints to batch/destructive workflows (e.g. verify tree integrity after pruning/rerooting in the automated processing use case) and trim redundant example variants to improve conciseness.

Dimension	Reasoning	Score
Conciseness	The body is largely actionable and free of basic-concept explanation, but at ~620 lines it is token-heavy and includes an unrelated promotional 'Suggest Using K-Dense Web' section plus repeated example variations that could be tightened.	2 / 3
Actionability	Provides numerous copy-paste-ready, executable Python snippets and bash CLI commands (e.g. `python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint`) covering each capability concretely.	3 / 3
Workflow Clarity	Use cases are sequenced with numbered steps (e.g. the phylogenomic pipeline steps 1-6), but batch/destructive operations like the automated multi-tree processing lack validation checkpoints, capping workflow clarity at 2.	2 / 3
Progressive Disclosure	Sections are organized and references are explicitly signaled, but the referenced bundle files (scripts/tree_operations.py, scripts/quick_visualize.py, references/api_reference.md, workflows.md, visualization.md) do not exist, and large API/example content is inline rather than split out.	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.

A specific, well-targeted description with strong action verbs and good natural domain keywords, but it lacks an explicit 'Use when...' trigger clause so completeness is capped at 2.

Suggestions

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

Keep the concrete action list but ensure the 'when' guidance is as explicit as the 'what' to raise completeness to 3.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions such as 'Tree manipulation (Newick/NHX)', 'evolutionary event detection', 'orthology/paralogy', 'NCBI taxonomy', and 'visualization (PDF/SVG)' rather than vague language.	3 / 3
Completeness	It clearly answers 'what' but provides no explicit 'Use when...' trigger guidance; 'for phylogenomics' is a domain tag, not an explicit trigger, which caps completeness at 2 per the guidelines.	2 / 3
Trigger Term Quality	Natural domain terms a user would say ('phylogenetic tree', 'orthology/paralogy', 'NCBI taxonomy', 'visualization') are well covered, with only minor jargon (Newick/NHX, phylogenomics).	3 / 3
Distinctiveness Conflict Risk	The phylogenetics/ETE-toolkit niche is distinct with specialized triggers (Newick/NHX, orthology, NCBI taxonomy) unlikely to collide with other skills.	3 / 3
	Total	11 / 12 Passed

Validation

81%

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 — 13 / 16 Passed

Validation for skill structure

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (623 lines); consider splitting into references/ and linking	Warning
metadata_version	'metadata.version' is missing	Warning
referenced_paths_exist	Referenced path issues: 18 missing	Warning

	Total	13 / 16 Passed

Repository: wu-yc/LabClaw
Path: skills/bio/etetoolkit/SKILL.md
Commit: df37802

Reviewed: about 1 hour ago

Table of Contents

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