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 thesecondfox/skill --skill bio-ecological-genomics-species-delimitationgit clone --depth 1 https://github.com/thesecondfox/skillWrote 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/thesecondfox/skill/bio-ecological-genomics-species-delimitation)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-ecological-genomics-species-delimitation"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-ecological-genomics-species-delimitation/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/thesecondfox/skill/bio-ecological-genomics-species-delimitation"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-ecological-genomics-species-delimitation.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 | $0.00094 | $0.03087 |
| Opus 5 | $0.00047 | $0.01543 |
| Sonnet 5 | $0.00019 | $0.00617 |
| Haiku 4.5 | $0.00009 | $0.00309 |
Grade A, and why
bio-ecological-genomics-species-delimitation 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 11d 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 — 325 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: BioPython 1.83+, numpy 1.26+, scipy 1.12+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - 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.
Species Delimitation
"Delineate species boundaries from my DNA barcoding data" → Apply multiple delimitation methods (distance-based ASAP, tree-based bPTP/GMYC, coalescent BPP) to molecular data and compare results for multi-method consensus following integrative taxonomy best practice.
- CLI: ASAP web tool or standalone for distance-based partitioning
- Python: bPTP via
PTP-pyqt5for Bayesian branching-rate analysis - R:
splits::gmyc()for coalescent/speciation transition model
Delimits putative species from molecular data using complementary distance-based, tree-based, and coalescent methods.
Overview of Methods
| Method | Input | Approach | Strengths | Limitations |
|---|---|---|---|---|
| ASAP | Aligned sequences | Distance-based partitioning | Fast, automatic, ranks partitions | Single locus only |
| bPTP | Rooted phylogeny | Bayesian branching rates | Bayesian support values | Over-splits with structure |
| GMYC | Ultrametric tree | Coalescent/speciation transition | Well-established theory | Requires ultrametric tree |
| BPP | Multi-locus alignment | Full coalescent model | Multi-locus, statistically rigorous | Computationally intensive |
ASAP (Assemble Species by Automatic Partitioning)
Goal: Partition aligned barcode sequences into putative species using pairwise genetic distances.
Approach: Run ASAP with a substitution model (K2P, p-distance) and rank candidate partitions by asap-score.
What ships with it
1 file 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.
- 11d ago First seen · 325 lines · 94 tokens per session scan A ff18c65e696f
bio-ecological-genomics-species-delimitation is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 94 tokens to every session and 3,087 once invoked, about $0.0005 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 2026-08-31.
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