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 PKU-YuanGroup/OpenAI4S --skill bio-comparative-genomics-positive-selectiongit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-comparative-genomics-positive-selection)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-comparative-genomics-positive-selection"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-positive-selection/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/pku-yuangroup/openai4s/bio-comparative-genomics-positive-selection"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-positive-selection.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 | $0.00243 | $0.10679 |
| Opus 5 | $0.00121 | $0.05339 |
| Sonnet 5 | $0.00049 | $0.02136 |
| Haiku 4.5 | $0.00024 | $0.01068 |
Grade A, and why
bio-comparative-genomics-positive-selection scanned grade A with 1 finding 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 8d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
# MACSE V2: wget https://bioweb.supagro.inra.fr/macse/releases/macse_v2.07.jar This is a copy
98% identical to bio-comparative-genomics-positive-selection — 14 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 503 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: PAML 4.10.7+, HyPhy 2.5.62+ (BUSTED-MH from Lucaci 2023 MBE 40:msad150; FUBAR-MH from same), datamonkey.org 2024+ for web jobs, IQ-TREE 2.3.6+, MACSE V2.07+, PRANK 170427+, MAFFT 7.526+, PREQUAL 1.02+, HmmCleaner 0.243+, GARD (HyPhy bundled), RDP5 5.59+, ete4 4.1.0+, BioPython 1.84+, scipy 1.13+, polyDFE 2.0+, DFE-alpha 2.16+, GRAPES 1.1.1+, RERconverge 0.3.0+, CSUBST 1.6.0+, PhyloAcc 2.4.0+. Quest-for-Selection benchmark refreshed annually.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
codeml(PAML; check bycodeml /dev/null-- prints version banner),hyphy --version,gard --help - Python:
pip show pyhyphy; introspect ete4 API for tree-labeling - R:
packageVersion('RERconverge');?correlateWithBinaryPhenotype
If code throws branch-site test LRT non-positive, omega2 hit upper bound 999, MEME ML mixed gradient, the most common cause is alignment error or saturated dS -- inspect alignment with TCS / Guidance2 and dS-vs-divergence-time. PAML 4.10 changed several control-file keywords from 4.9 (getSE = 1 syntax tightened).
Positive Selection Analysis
"Is this gene / branch / site under positive selection?" -> dN/dS (omega = nonsynonymous-to-synonymous substitution rate ratio) framework with explicit choice of WHICH question is being asked (gene-wide / branch-specific / site-specific / episodic) and WHICH null is being rejected. The "test failed because of selection" claim has more known confounders than any other comparative-genomics inference; mandatory pre-screens are: recombination (GARD), alignment errors (PREQUAL or HmmCleaner), saturation (dS distribution), and gBGC (W->S substitution bias). Skipping any one inflates Type-I error to ~20-50% (Anisimova & Yang 2007 MBE 24:1219; Pond 2006 Mol Biol Evol 23:1891).
- CLI:
codemlPAML site, branch, branch-site models - CLI:
hyphy bustedhyphy memehyphy felhyphy fubarhyphy absrelhyphy relaxhyphy gard - Web: datamonkey.org for HyPhy jobs without local install
- R:
RERconverge::correlateWithBinaryPhenotype()for trait-rate associations - CLI:
csubst analyzefor convergent substitution - R/CLI:
phyloaccfor noncoding accelerated evolution
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- 8d ago First seen · 503 lines · 243 tokens per session scan A 604b390fba92
bio-comparative-genomics-positive-selection is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed today), licensed MIT. It adds 243 tokens to every session and 10,679 once invoked, about $0.0012 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 98% identical to bio-comparative-genomics-positive-selection, differing in 14 lines, and is treated as a copy.
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