etetoolkit

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

1.37x

Quality

66%

Does it follow best practices?

Impact

85%

1.37x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/etetoolkit/SKILL.md

Quality

Discovery

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.

This is a strong, domain-specific description that excels at listing concrete capabilities and using natural trigger terms from the bioinformatics/phylogenetics domain. Its main weakness is the absence of an explicit 'Use when...' clause, which would help Claude know precisely when to select this skill. The description is concise and avoids fluff, using appropriate third-person voice.

Suggestions

Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about phylogenetic trees, tree visualization, evolutionary analysis, or mentions ETE, Newick, or NCBI taxonomy.'

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions: tree manipulation with format details (Newick/NHX), evolutionary event detection, orthology/paralogy analysis, NCBI taxonomy integration, and visualization with output formats (PDF/SVG).	3 / 3
Completeness	Clearly answers 'what does this do' with specific capabilities, but lacks an explicit 'Use when...' clause or equivalent trigger guidance. The when is only implied by the domain terms listed.	2 / 3
Trigger Term Quality	Includes strong natural keywords users would say: 'phylogenetic tree', 'ETE', 'Newick', 'NHX', 'orthology', 'paralogy', 'NCBI taxonomy', 'phylogenomics', 'PDF/SVG'. These are the exact terms bioinformatics users would use when requesting this functionality.	3 / 3
Distinctiveness Conflict Risk	Highly distinctive niche — phylogenetic trees, ETE toolkit, Newick/NHX formats, orthology/paralogy, and NCBI taxonomy are very specific to computational phylogenetics and unlikely to conflict with other skills.	3 / 3
	Total	11 / 12 Passed

Implementation

50%

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

This skill is highly actionable with excellent, executable code examples covering the full breadth of ETE toolkit capabilities. However, it is far too verbose for a SKILL.md overview—much of the detailed content (clustering, tree comparison, advanced visualization) should live in the referenced files rather than inline. The lack of validation checkpoints in batch/multi-step workflows is a notable gap.

Suggestions

Move detailed sections (Clustering Analysis, Tree Comparison, Advanced Visualization) into the referenced files (workflows.md, visualization.md) and keep only brief summaries with links in SKILL.md

Remove redundant code examples—the phylogenomic pipeline use case largely duplicates Section 2's phylogenetic analysis code

Add explicit validation/error-handling steps to batch workflows (Use Case 4), such as try/except blocks and verification that output files were created correctly

Trim the Best Practices section to only non-obvious tips—items like 'use PDF/SVG for publications' and 'use PhyloTree for phylogenetics' are self-evident

Dimension	Reasoning	Score
Conciseness	The skill is extremely verbose at ~400+ lines, with significant redundancy. Multiple code examples repeat similar patterns (e.g., ortholog detection appears in both Section 2 and Use Case 1). The overview section explains what ETE is, which Claude already knows. Many sections could be condensed or moved to reference files.	1 / 3
Actionability	The skill provides fully executable, copy-paste ready Python code and CLI commands throughout. Code examples are complete with imports, concrete file paths, and realistic parameters. Every capability section includes working code patterns.	3 / 3
Workflow Clarity	Multi-step workflows are present (e.g., Use Case 1 has numbered steps, tree preprocessing pipeline), but they lack explicit validation checkpoints. For batch operations like Use Case 4 (automated tree analysis processing multiple files), there are no validation steps or error handling for malformed trees or failed operations.	2 / 3
Progressive Disclosure	The skill does reference external files (api_reference.md, workflows.md, visualization.md) in a Reference Documentation section, but the main SKILL.md contains enormous amounts of inline content that should be in those reference files. The visualization section alone could be its own reference, and the clustering/comparison sections add significant bulk.	2 / 3
	Total	8 / 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 — 9 / 11 Passed

Validation for skill structure

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (622 lines); consider splitting into references/ and linking	Warning
metadata_version	'metadata.version' is missing	Warning

	Total	9 / 11 Passed

Repository: K-Dense-AI/claude-scientific-skills
Commit: 25e1c0f

Reviewed: 4 days ago

Table of Contents

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