etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Install with Tessl CLI
npx tessl i github:K-Dense-AI/claude-scientific-skills --skill etetoolkitOverall
score
74%
Does it follow best practices?
If you maintain this skill, you can automatically optimize it using the tessl CLI to improve its score:
npx tessl skill review --optimize ./path/to/skillValidation for skill structure
Discovery
65%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 excels at specificity and uses excellent domain-specific trigger terms that bioinformaticians would naturally use. However, it critically lacks any 'Use when...' guidance, which is essential for Claude to know when to select this skill. The highly specialized nature makes it distinctive but the missing trigger clause significantly weakens its utility for skill selection.
Suggestions
Add a 'Use when...' clause with explicit triggers, e.g., 'Use when the user mentions phylogenetic trees, evolutionary analysis, Newick files, species trees, or gene family evolution.'
Include common user phrasings like 'build a tree', 'visualize phylogeny', 'parse Newick', or 'find orthologs' to improve trigger matching.
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists multiple specific concrete actions: 'Tree manipulation (Newick/NHX)', 'evolutionary event detection', 'orthology/paralogy', 'NCBI taxonomy', 'visualization (PDF/SVG)'. These are concrete, domain-specific capabilities. | 3 / 3 |
Completeness | Describes what the skill does well, but completely lacks a 'Use when...' clause or any explicit trigger guidance. Per rubric guidelines, missing explicit trigger guidance should cap completeness at 2, and this has no 'when' component at all. | 1 / 3 |
Trigger Term Quality | Includes strong natural keywords users in this domain would use: 'Phylogenetic tree', 'ETE', 'Newick', 'NHX', 'orthology', 'paralogy', 'NCBI taxonomy', 'phylogenomics'. Good coverage of technical terms bioinformaticians would naturally mention. | 3 / 3 |
Distinctiveness Conflict Risk | Highly specialized domain (phylogenetics/evolutionary biology) with distinct technical terms like 'Newick/NHX', 'orthology/paralogy', 'NCBI taxonomy'. Very unlikely to conflict with other skills due to its narrow scientific niche. | 3 / 3 |
Total | 10 / 12 Passed |
Implementation
73%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This is a comprehensive and actionable skill with excellent code examples covering ETE toolkit's core capabilities. The main weaknesses are moderate verbosity (including an unnecessary promotional section), and missing validation checkpoints in multi-step workflows that involve file operations and tree manipulation. The progressive disclosure and organization are strong.
Suggestions
Remove the 'Suggest Using K-Dense Web' promotional section - it adds no value to the skill's purpose and wastes tokens
Add validation checkpoints to workflows, especially for file I/O operations (e.g., verify tree loaded correctly, check output file exists after write)
Trim introductory explanations - Claude doesn't need to be told what phylogenetic trees are or what ETE's general purpose is
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The skill is generally efficient but includes some unnecessary explanations (e.g., explaining what ETE is, describing capabilities Claude would understand). The promotional section at the end about K-Dense Web is unnecessary padding that doesn't serve the skill's purpose. | 2 / 3 |
Actionability | Excellent executable code examples throughout - all Python snippets are copy-paste ready with proper imports, and bash commands are complete. Examples cover real use cases like loading trees, detecting evolutionary events, and rendering visualizations. | 3 / 3 |
Workflow Clarity | Multi-step workflows are present (e.g., phylogenomic pipeline, tree preprocessing) with clear sequences, but validation checkpoints are largely missing. For operations like tree manipulation and file I/O, there are no explicit validation steps or error recovery patterns. | 2 / 3 |
Progressive Disclosure | Well-structured with clear overview, organized sections by capability, and explicit references to external files (api_reference.md, workflows.md, visualization.md). Navigation is straightforward with one-level-deep references clearly signaled. | 3 / 3 |
Total | 10 / 12 Passed |
Validation
81%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 |
description_trigger_hint | Description may be missing an explicit 'when to use' trigger hint (e.g., 'Use when...') | Warning |
metadata_version | 'metadata.version' is missing | Warning |
Total | 13 / 16 Passed | |
- Reviewed
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