etetoolkit

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

Quality

71%

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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

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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 comprehensive executable examples and good progressive-disclosure structure pointing to real reference files. Its main weaknesses are noticeable code duplication between Core Capabilities and Use Cases, and missing validation checkpoints on batch/destructive tree operations.

Suggestions

Collapse the duplicated code in Common Use Cases by referencing the relevant Core Capabilities section instead of restating the same tree_operations.py commands and PhyloTree workflow.

Add explicit validation checkpoints to batch and destructive workflows, e.g. "After pruning/rerooting, verify leaf count and topology with `python scripts/tree_operations.py stats` before proceeding."

Move the bulk of the inline visualization and clustering examples into the existing references/ files, keeping SKILL.md as a leaner overview with one or two quick-start snippets.

Dimension	Reasoning	Score
Conciseness	The body is mostly efficient and code-focused, but the Common Use Cases section substantially duplicates code already shown in Core Capabilities (e.g. tree_operations.py commands and the PhyloTree workflow), adding length that could be trimmed.	3 / 5
Actionability	Provides extensive copy-paste-ready Python and bash examples covering tree manipulation, phylogenetic analysis, taxonomy, visualization, clustering, and comparison across the common cases.	5 / 5
Workflow Clarity	Numbered sequences are present (e.g. Use Case 1 steps 1–6), but batch and destructive operations — Automated Tree Analysis deletes nodes across many trees, and pruning/rerooting modifies trees — lack validation checkpoints, capping this at 3.	3 / 5
Progressive Disclosure	References to real one-level-deep files (references/api_reference.md, workflows.md, visualization.md and scripts/tree_operations.py, quick_visualize.py) are clearly signaled with descriptions, but the SKILL.md body is long and inline-heavy, keeping it just short of a clean 5.	4 / 5
	Total	15 / 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.

The description is specific, distinctive, and rich in domain trigger terms, but it lacks an explicit "Use when…" clause that tells Claude when to invoke the skill. Adding concrete trigger guidance would raise the completeness score.

Suggestions

Add an explicit "Use when…" clause, e.g. "Use when working with phylogenetic trees, Newick/NHX files, gene-tree reconciliation, orthology detection, or NCBI taxonomy lookup."

Include common user phrasings like "phylogeny", "gene tree", "species tree", and "tree of life" to broaden natural trigger coverage.

Mention the .nw/.nwk Newick file extensions alongside Newick/NHX to improve trigger-term file-extension coverage.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete capabilities — "Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG)" — giving comprehensive coverage rather than only minor gaps.	5 / 5
Completeness	Has a clear "what" but no explicit "Use when…" trigger clause; "for phylogenomics" only weakly implies when, so completeness is capped at 3 per the judging guidelines.	3 / 5
Trigger Term Quality	Strong natural domain keywords with synonyms and formats (phylogenetic tree, Newick/NHX, orthology/paralogy, NCBI taxonomy, PDF/SVG, phylogenomics), but misses common variations a user might say such as phylogeny, gene tree, or species tree.	4 / 5
Distinctiveness Conflict Risk	A clear niche (ETE phylogenetic toolkit) with highly domain-specific triggers (Newick, NHX, orthology/paralogy, phylogenomics) and minimal risk of firing for the wrong skill.	5 / 5
	Total	17 / 20 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: 3a6c3a9

Reviewed: 1 day ago

Table of Contents

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