Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add Hongda-Zhao/bio-gene-to-reference-tree --skill gene-tree-query-and-scopegit clone --depth 1 https://github.com/Hongda-Zhao/bio-gene-to-reference-treeWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/hongda-zhao/bio-gene-to-reference-tree/gene-tree-query-and-scope)<a href="https://agentmods.dev/skills/hongda-zhao/bio-gene-to-reference-tree/gene-tree-query-and-scope"><img src="https://agentmods.dev/badge/skills/hongda-zhao/bio-gene-to-reference-tree/gene-tree-query-and-scope/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/hongda-zhao/bio-gene-to-reference-tree/gene-tree-query-and-scope"><img src="https://agentmods.dev/badge/skills/hongda-zhao/bio-gene-to-reference-tree/gene-tree-query-and-scope.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00057 | $0.00268 |
| Opus 5.5 | $0.00023 | $0.00107 |
| Sonnet 5.5 | $0.00011 | $0.00054 |
| Haiku 4.5 | $0.00006 | $0.00027 |
Grade A, and why
gene-tree-query-and-scope scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Gene-Tree Query and Scope
This repository-level adapter delegates its scientific rules to the canonical Skill.
- Read the core claims and workflow gates.
- Follow Step 1 — Resolve the query.
- After Gate 1 passes, follow Step 2 — Define the objective.
- Load sequence-type routing or taxonomy resolution only when its canonical trigger applies.
When both linked exit conditions are satisfied, hand off to the reference-curation adapter.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 16 lines · 57 tokens per session scan A 22ebc231a93f
gene-tree-query-and-scope is a skill published in the GitHub repository Hongda-Zhao/bio-gene-to-reference-tree (17 stars, last pushed 2mo ago), licensed MIT. It adds 57 tokens to every session and 268 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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