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 GPTomics/bioSkills --skill introgression-detectiongit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/introgression-detection)<a href="https://agentmods.dev/skills/gptomics/bioskills/introgression-detection"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/introgression-detection/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/gptomics/bioskills/introgression-detection"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/introgression-detection.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 | $0.00241 | $0.08275 |
| Opus 5 | $0.00120 | $0.04137 |
| Sonnet 5 | $0.00048 | $0.01655 |
| Haiku 4.5 | $0.00024 | $0.00827 |
Grade A, and why
bio-comparative-genomics-introgression-detection 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 7d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-comparative-genomics-introgression-detection — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 481 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: Dsuite 0.5+ (millanek/Dsuite; Malinsky 2021 Mol Ecol Res 21:584; ABBAclustering option from Koppetsch-Malinsky-Matschiner 2024 Syst Biol), HyDe 0.4.3+ (Blischak 2018 Syst Biol 67:821), QuIBL (Edelman 2019 Science 366:594), TreeMix 1.13+ (Pickrell & Pritchard 2012 PLoS Genet 8:e1002967), sprime (Browning 2018 Cell 173:53), Twisst (Martin & Van Belleghem 2017 Genetics 206:429), PhyloNet 3.8.2+ (NakhlehLab/PhyloNet; Than-Ruths-Nakhleh 2008 BMC Bioinf 9:322) and PhyloNetworks 0.16+ (JuliaPhylo/PhyloNetworks; Solis-Lemus, Bastide & Ane 2017 MBE 34:3292), qpAdm / qpGraph (AdmixTools v2.0+; Maier 2023), ADMIXTOOLS2 R wrapper (Maier 2023 eLife 12:e85492), MaCS-like simulators (msprime 1.3+ for testing), bcftools 1.21+, samtools 1.21+, vcftools 0.1.16+, R 4.4+. See upstream Dsuite docs for visualization helpers.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
Dsuite --version;treemix --help;qpDstat --help(AdmixTools) - Python:
pip show msprime hyde - R:
packageVersion('admixtools')
If code throws Dsuite SETS file format error, TreeMix matrix singular, qpAdm rotation failed, these tools share strict input requirements: Dsuite needs a SETS file mapping samples to populations + an outgroup; TreeMix needs allele-frequency matrix; qpAdm needs ind / snp / geno trio (EIGENSTRAT format).
Introgression and Admixture Detection
"Has there been gene flow between these species / populations?" -> Tests for inter-population admixture span site-frequency (ABBA-BABA, f4), tree-topology (Dsuite f-branch, QuIBL, Twisst), explicit-network (PhyloNet), and haplotype-tract (sprime) approaches. The fundamental confounder is incomplete lineage sorting (ILS): under a symmetric tree with no gene flow, the ABBA and BABA patterns occur with equal frequency from ancestral polymorphism. A significant D-statistic indicates EITHER (a) introgression, OR (b) ancestral structure, OR (c) sampling from a ghost lineage -- additional evidence is required to distinguish (Green 2010 Science 328:710; Durand 2011 MBE 28:2239; Eriksson & Manica 2012 PNAS 109:13956). For high-confidence claims, combine D-statistic with f-branch mapping (assigns admixture to specific branches), Twisst / QuIBL topology-weighting, and TreeMix migration edges.
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.
- 7d ago First seen · 481 lines · 241 tokens per session scan A 2be46194c992
bio-comparative-genomics-introgression-detection is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 241 tokens to every session and 8,275 once invoked, about $0.0012 per session on Opus 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 2026-09-03.
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