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 conservation-geneticsgit 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/conservation-genetics)<a href="https://agentmods.dev/skills/gptomics/bioskills/conservation-genetics"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/conservation-genetics/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/conservation-genetics"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/conservation-genetics.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 | $0.00232 | $0.07891 |
| Opus 5 | $0.00116 | $0.03946 |
| Sonnet 5 | $0.00046 | $0.01578 |
| Haiku 4.5 | $0.00023 | $0.00789 |
Grade A, and why
bio-ecological-genomics-conservation-genetics 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 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.
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.
How it starts
The opening of the file, as written. The whole thing — 435 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: hierfstat 0.5+, adegenet 2.1+, detectRUNS 2.0+, poppr 2.9+, NeEstimator V2.1+, GONE2, SNeP 1.1+, SLiM 4+, msprime 1.3+, bcftools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('<pkg>')then?function_nameto verify parameters - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Conservation Genetics
"Assess the genetic health of my endangered population" -> Estimate Ne by time horizon (contemporary LD, recent trajectory, deep demographic history), measure inbreeding via F_ROH with length-class thresholds, decompose realized vs masked genetic load, and interpret against the modern 100/1000 Ne rule.
- R:
hierfstat::basic.stats()for F-statistics and diversity - R:
detectRUNS::consecutiveRUNS.run()orbcftools roh -G30for ROH detection - CLI:
Ne2.exe option_file.ne2for NeEstimator V2 contemporary Ne (option-file driven, NOT CLI flags) - CLI:
gone2for recent Ne trajectory from genome-wide LD (requires populated cM map)
The Single Most Important Modern Insight -- There is No Single Best Ne Estimator
The most common methodological failure in conservation genetics is treating "Ne" as one quantity. It is not. Each Ne estimator captures a different time horizon with different biases:
- LD-based (NeEstimator V2, Waples 2006): Last 1-few generations; biased downward at small N
- GONE / GONE2 (Santiago 2020): Recent 100-200 generations trajectory; requires populated cM genetic map
- Heterozygote-excess: Last 1 generation only; very low power
- Temporal (Jorde-Ryman): Between two time-sampled cohorts
- Stairway Plot 2 / dadi / fastsimcoal2: 10^3 to 10^5 generations from SFS
- PSMC: 10^4 to 10^6 generations from single high-coverage genome
What ships with it
3 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 · 435 lines · 232 tokens per session scan A 91abd9543a9f
bio-ecological-genomics-conservation-genetics is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 232 tokens to every session and 7,891 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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