etetoolkit

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

Quality

72%

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 ./backend/cli/skills/biology/etetoolkit/SKILL.md

Quality

Content

70%

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 and well-structured with solid progressive disclosure, but its length and redundancy (especially around visualization and repeated CLI examples) cost conciseness, and its workflows lack the validation checkpoints expected for destructive/batch tree operations.

Suggestions

Add explicit validation/re-verification checkpoints to destructive and batch workflows (e.g. confirm topology or leaf count after prune/delete before saving).

Consolidate duplicated visualization guidance — keep a concise example inline and defer the rest to references/visualization.md rather than repeating in Use Case 3.

Trim or cross-reference the repeated tree_operations.py command blocks so each command is documented once.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with executable, task-oriented code and no over-explanation of basic concepts, but it is lengthy (~610 lines) with notable redundancy — visualization is shown inline, repeated in Use Case 3, and again in references/visualization.md, and several tree_operations.py commands are restated across sections.	2 / 3
Actionability	Provides fully executable Python and bash throughout — concrete imports, method calls, and CLI commands with specific flags (e.g. `--keep-taxa`, `--in-format 0`) that are copy-paste ready.	3 / 3
Workflow Clarity	Sequenced numbered workflows exist (e.g. the Phylogenomic Pipeline steps 1-6), but destructive/batch operations like pruning, deleting low-support nodes, and resolve_polytomy lack explicit validate-then-proceed checkpoints, so workflow clarity is capped at 2 per the rubric.	2 / 3
Progressive Disclosure	SKILL.md serves as a clear overview with well-signaled, one-level-deep references to real files (references/api_reference.md, workflows.md, visualization.md) and pointed-to scripts, giving easy navigation without nested reference chains.	3 / 3
	Total	10 / 12 Passed

Description

75%

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, action-dense, and highly distinctive, but it omits an explicit "Use when..." trigger clause, which caps completeness at 2 despite strong coverage of natural terminology.

Suggestions

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

Include common file extensions a user might mention (e.g. .nwk, .nhx, .tree) to broaden trigger coverage.

Tighten the trailing "for phylogenomics" into a concrete usage context rather than a loose domain tag.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions including "Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG)", matching the multi-action anchor.	3 / 3
Completeness	Clearly states what the skill does, but there is no "Use when..." clause or equivalent explicit trigger guidance; the trailing "for phylogenomics" is a weak domain tag rather than explicit when-guidance, so completeness is capped at 2 per the rubric guideline.	2 / 3
Trigger Term Quality	Good coverage of natural domain terms a user would say — "phylogenetic tree", "Newick/NHX", "orthology/paralogy", "NCBI taxonomy", "PDF/SVG", "phylogenomics" — with little jargon-only padding.	3 / 3
Distinctiveness Conflict Risk	A clearly defined niche (ETE phylogenetic toolkit) with distinctive triggers (Newick/NHX, orthology/paralogy, NCBI taxonomy) making it unlikely to fire for unrelated 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
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	13 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/biology/etetoolkit/SKILL.md
Commit: 52845c3

Reviewed: about 11 hours ago

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