busco-phylogeny
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation
52
57%
Does it follow best practices?
Impact
—
No eval scenarios have been run
Advisory
Suggest reviewing before use
Optimize this skill with Tessl
npx tessl skill review --optimize ./phylo_from_buscos/SKILL.mdQuality
Discovery
67%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 technically precise and occupies a clear niche in computational phylogenomics, making it highly distinctive. Its main weaknesses are the absence of an explicit 'Use when...' clause and missing common user-facing trigger term variations (e.g., 'phylogenetic tree', 'species tree', 'SLURM'). Adding these would significantly improve skill selection accuracy.
Suggestions
Add an explicit 'Use when...' clause, e.g., 'Use when the user wants to build phylogenetic trees from genome assemblies, run BUSCO analyses, or create phylogenomic pipelines.'
Include common user-facing trigger term variations such as 'phylogenetic tree', 'species tree', 'comparative genomics', 'SLURM', 'HPC', 'evolutionary relationships', and 'ortholog extraction'.
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists specific concrete actions: 'Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs' and 'scheduler-aware workflow generation'. These are precise, domain-specific capabilities. | 3 / 3 |
Completeness | Clearly answers 'what does this do' (generate phylogenies from genome assemblies using specific tools and workflow generation), but lacks an explicit 'Use when...' clause or equivalent trigger guidance, which caps this at 2 per the rubric. | 2 / 3 |
Trigger Term Quality | Includes strong domain-specific keywords like 'phylogenies', 'genome assemblies', 'BUSCO', 'compleasm', 'single-copy orthologs', and 'scheduler-aware workflow'. However, it misses common user variations like 'phylogenetic tree', 'species tree', 'comparative genomics', 'HPC', 'SLURM', or 'evolutionary analysis'. | 2 / 3 |
Distinctiveness Conflict Risk | Highly distinctive niche combining phylogenomics, BUSCO/compleasm orthologs, and scheduler-aware workflows. This is unlikely to conflict with other skills due to its very specific bioinformatics domain focus. | 3 / 3 |
Total | 10 / 12 Passed |
Implementation
47%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This skill demonstrates strong workflow design with clear sequencing, validation checkpoints, and comprehensive coverage of a complex phylogenomics pipeline. However, it severely suffers from verbosity—explaining concepts Claude already knows (assembly quality metrics, RefSeq vs GenBank), repeating references to REFERENCE.md dozens of times, and including detailed sub-workflows that belong in reference files. The actionability is moderate since many steps defer to external templates and references rather than providing complete inline guidance.
Suggestions
Drastically reduce content by moving STEP 0A (NCBI query with quality filtering details), the substitution model recommendation system, and the detailed script validation workflow into reference files, keeping only brief summaries with links in SKILL.md
Remove explanations of concepts Claude already knows: what N50 is, what RefSeq vs GenBank means, what assembly levels are, what BUSCO scores indicate—these add hundreds of tokens without value
Consolidate the repeated 'see references/REFERENCE.md' directives into a single reference table at the top mapping each step to its reference section, rather than repeating the directive in every step
Reduce the 'Important Notes' section which largely duplicates instructions already given in the body—either keep the notes section OR the inline instructions, not both
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | Extremely verbose at ~600+ lines. Contains extensive explanations of concepts Claude already knows (what RefSeq vs GenBank is, what N50 means, what assembly levels are), redundant reminders ('ALWAYS', 'IMPORTANT'), and massive repetition of references to REFERENCE.md. Many sections could be condensed to a fraction of their size. | 1 / 3 |
Actionability | Provides some concrete commands (compleasm, MAFFT, IQ-TREE, ASTRAL) and executable code snippets, but heavily relies on external templates and REFERENCE.md for actual implementation details. Many steps say 'see references/REFERENCE.md for detailed implementation' rather than providing the concrete guidance inline. The template system adds indirection. | 2 / 3 |
Workflow Clarity | The workflow is clearly sequenced from Step 0 through Step 9 with explicit input/output mappings between steps. The Script Validation section provides a thorough feedback loop with pipeline continuity verification, resource compatibility checks, and structured error reporting. Validation checkpoints are explicit and well-defined. | 3 / 3 |
Progressive Disclosure | Good use of references to REFERENCE.md and templates directory for detailed content, but the SKILL.md itself is far too long and includes content that should be in reference files (e.g., the entire STEP 0A section with assembly quality considerations, the detailed substitution model recommendation process, the extensive validation workflow). The main file should be a concise overview pointing to these details. | 2 / 3 |
Total | 8 / 12 Passed |
Validation
90%Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.
Validation — 10 / 11 Passed
Validation for skill structure
| Criteria | Description | Result |
|---|---|---|
skill_md_line_count | SKILL.md is long (820 lines); consider splitting into references/ and linking | Warning |
Total | 10 / 11 Passed | |
- Repository
- brunoasm/my_claude_skills
- Commit
2a19b68
- Reviewed
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