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AC tooluniverse-phylogenetics

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nexus/Newick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 12 files · 3 scripts body ≈ 3 974 tokens Open the sourcegithub.com↗ analyzed 11 h ago

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

As a process C 54/100 · Has gaps — weak spots: result and completion, inputs and preconditions, failures and branches

AnalyzerData and analyticstype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
A
98/100
safety, quality, tests
Safety 60%
100
Quality 40%
95
Run on models
none yet
Process rating
C
54/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Failures and branches w 10
0
the three weakest of ten parameters · all ten

How to improve

    For the model run — optional
    • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
    • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

    Guard findings · 0

    ✓ No critical or high findings

    Files scanned: 11. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    ✓ No remarks against the Agent Skills spec

    Process rating: all ten parameters 54/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 0Failures and branches. Linear process with no failure handling
    • 0Progress reporting. Says nothing while it works
    • 60Tools and files. Uses tools (bash, python) that frontmatter does not declare
    • 85Steps. 46 steps, 3 vague phrases
    • 100When it triggers. States when to use and when not to
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 3974 tokens
    • 100Running it twice. No mutating operations
    • low 16 top-level sections: this looks like several domains in one skill

    Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

    Quality signals

    • +5Description has no quoted example phrases that should trigger the skill
    • +3Output format is not stated: the model decides each time
    • +1No license
    • +2Single-language instructions
    • +4Description says when NOT to use the skill
    • +3Description length 754: enough signal without eating the budget
    • +4Structure: 28 headings
    • +3Step-by-step instructions: 46 items
    • +4Has examples (13 code blocks)
    • +4Reference files are cited in the instructions (4 of 4)
    • +3All 2 scripts are documented

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 95.