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AD phylogenetics

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.

K-Dense-AI/claude-scientific-skills Agent Skills author: K-Dense-AI MIT 3 files · 1 script body ≈ 2 156 tokens Open the sourcegithub.com↗ analyzed 12 h ago

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree…

As a process D 45/100 · Unfinished process — weak spots: result and completion, when it triggers, inputs and preconditions

AnalyzerGitHubSoftware developmentData and analyticsWriting and documentstype 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
96/100
safety, quality, tests
Safety 60%
99
Quality 40%
92
Run on models
none yet
Process rating
D
45/100
Unfinished process
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 · 1

    ✓ No critical or high findings

    Medium and low: 1
    • low Concealment en-hide-from-user SKILL.md:92
      Instruction to hide actions from the user (negated — the text forbids it)
      must stop the trimming step; do not silently copy the untrimmed input under a
      negated

    Files scanned: 3. 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 45/100

    • 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
    • 20When it triggers. No condition that starts the skill
    • 30Running it twice. 5 mutating operations with no state check
    • 60Tools and files. Uses tools (python) that frontmatter does not declare
    • 100Steps. 10 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2156 tokens
    • 100Progress reporting. Reports progress

    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
    • +4Description does not say when NOT to use the skill (false activations)
    • +3Output format is not stated: the model decides each time
    • +2Single-language instructions
    • +3Description length 368: enough signal without eating the budget
    • +4Structure: 10 headings
    • +3Step-by-step instructions: 10 items
    • +4Has examples (5 code blocks)
    • +4Reference files are cited in the instructions (1 of 1)
    • +3All 1 scripts are documented
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 92.

    In the sandbox Скрипты не запустились

    The skill's scripts were run in a throwaway machine: no network, fake keys in the home directory, a tracer watching. We wrote down what they did. Reaching for the network or for secrets caps the technical grade at C; a quiet run adds no points.

    Запущено 1 скрипт; каждому дали двадцать секунд, поддельный домашний каталог с ключами и сеть, в которой ничего нет.

    Ни один не дошёл до работы — им не хватило зависимостей, аргументов или файлов. Это не отзыв о поведении: наблюдать было не за чем.

    scripts/phylogenetic_analysis.pyне запустился: phylogenetic_analysis.py: error: the following arguments are required: input

    5 Oct 2026