biopython-phylo

Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

Quality

76%

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Securityby

Passed

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tessl review fix ./scientific-skills/Data Analysis/biopython-phylo/SKILL.md

Quality

Content

65%Weight 40%Scale 1-5

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 a fully runnable example, but it loses points for redundant re-description in Implementation Details, missing validation checkpoints around destructive tree operations, and an orphaned reference bundle file that is never linked from the overview.

Suggestions

Add a validation/verification checkpoint after destructive steps — e.g., assert the reroot outgroup exists, verify the pruned taxon count, and confirm the converted output re-parses with Phylo.read before proceeding.

Link references/phylogenetics.md from the body (e.g., a '## Reference' section pointing to it for advanced topics like consensus trees, tree construction, and PhyloXML annotations) so the bundle file is discoverable.

Trim the 'Implementation Details' section to conventions not already shown in the code, removing the re-listing of prune/reroot/draw_ascii API calls to reduce redundancy.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with useful sections and no basic-concept padding, but the 'Implementation Details' section largely re-describes API calls already demonstrated in the runnable script (pruning, rerooting, draw_ascii, Agg backend), and the inlined ~120-line script could be trimmed, making it tighter than anchor 4 but not severely verbose.	3 / 5
Actionability	A complete, copy-paste-ready config plus `python scripts/phylo_task.py` script covers the common cases end-to-end (read, prune, reroot, convert, ASCII, stats, plot) with specific, executable Bio.Phylo calls.	5 / 5
Workflow Clarity	The main() sequence is clearly commented (Read → Manipulate → Write → ASCII → Stats → Plot), but destructive/batch operations (pruning taxa, rerooting) lack validation checkpoints or feedback loops; per the rubric cap, a destructive workflow without validation cannot exceed 3.	3 / 5
Progressive Disclosure	The body is well sectioned, but the provided bundle file references/phylogenetics.md (a 567-line reference) is never linked or signaled from SKILL.md, leaving a reference present but undiscoverable; this matches the anchor where references exist but are not clearly signaled.	3 / 5
	Total	14 / 20 Passed

Description

87%Weight 40%Scale 1-5

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 strong: it explicitly covers both capability and trigger conditions with concrete, domain-specific language and a clear niche. Minor gaps in action granularity and missing file-extension synonyms keep specificity and trigger_term_quality just below full marks.

Dimension	Reasoning	Score
Specificity	Names the library and several concrete actions ('read/write phylogenetic trees and perform visualization and statistics'), but 'visualization' and 'statistics' are bundled rather than individually enumerated, leaving minor coverage gaps versus the comprehensive anchor 5.	4 / 5
Completeness	Explicitly states both what it does ('read/write phylogenetic trees...visualization and statistics') and when to use it ('use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required') with concrete trigger phrases, matching the anchor 5 example.	5 / 5
Trigger Term Quality	The 'use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting' clause gives good natural keyword coverage, but omits common synonyms and file extensions (Newick, NEXUS, phyloXML, .nwk) that a user might actually say.	4 / 5
Distinctiveness Conflict Risk	Bio.Phylo phylogenetic tree manipulation is a clear, narrow niche with distinct triggers (pruning/rerooting, distance calculation, tree plotting) and minimal overlap risk with other skills.	5 / 5
	Total	18 / 20 Passed

Validation

87%

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 — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning
referenced_paths_exist	Referenced path issues: 3 missing	Warning

	Total	14 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/biopython-phylo/SKILL.md
Commit: f5ef65b

Reviewed: ~23 hours ago

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