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-whole-genome-alignmentgit 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-whole-genome-alignment)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-alignment/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-whole-genome-alignment"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-alignment.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 | $0.00237 | $0.07929 |
| Opus 5 | $0.00118 | $0.03964 |
| Sonnet 5 | $0.00047 | $0.01586 |
| Haiku 4.5 | $0.00024 | $0.00793 |
Grade A, and why
bio-comparative-genomics-whole-genome-alignment 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 9d 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.
This is a copy
94% identical to bio-comparative-genomics-whole-genome-alignment — 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 — 456 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: Progressive Cactus 2.9.1+ (ComparativeGenomicsToolkit/cactus; Armstrong 2020 Nature 587:246), Minigraph-Cactus (Hickey 2024 Nat Biotech 42:663; bundled with Cactus 2.5+), HAL toolkit 2.3+ (Hickey 2013 Bioinformatics 29:1341), LASTZ 1.04.22+, UCSC kentUtils for chain/net (Kent 2003 PNAS 100:11484), MUMmer 4.0.0+, minimap2 2.28+, AnchorWave 1.2.5+, progressiveMauve 2.4.0+, sibeliaz 1.2.5+, winnowmap 2.03+ (Jain 2022 Nat Methods 19:705). Toil workflow runner 6.0+ for Cactus on HPC/cloud.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
cactus --help,cactus-pangenome --help,halStats --help,lastz --version,nucmer --version,minimap2 --version - Python:
pip show toil,toil --version
If code throws Toil workflow restart failure, HAL file corrupted, WDL workflow missing, the Cactus pipeline is Toil-based and requires careful checkpointing; failed runs must be restarted with --restart. HAL file versions differ across hal-toolkit releases; pin the version that produced the file.
Whole Genome Alignment
"Align these multiple genomes at the base-pair level" -> Choose between reference-free progressive alignment (Cactus / Minigraph-Cactus: produces HAL, no privileged reference) and reference-anchored pairwise alignment (LASTZ chains/nets, MUMmer, minimap2: one genome is the reference, queries align to it). The fundamental tradeoff is scale vs structure: pairwise pipelines scale linearly per pair but lose multi-way relationships; progressive Cactus scales linearly with a tree but quadratically without and produces ancestrally-coherent alignments. For comparative genomics at vertebrate / mammal scale, Cactus is now the standard substrate (Zoonomia, Christmas 2023 Science 380:eabn3943; Bird10000 Genomes); for pangenome graph construction, Minigraph-Cactus (Hickey 2024) is the production pipeline.
- CLI:
cactus jobStore seqFile.txt output.hal --binariesMode local-- reference-free progressive WGA - CLI:
cactus-pangenome --reference ref name --vcf-- pangenome graph from genomes - CLI:
lastz target.fa[multiple] query.fathen UCSC chain-net pipeline -- pairwise to a reference - CLI:
minimap2 -ax asm5 ref.fa query.fa | samtools sort-- fast pairwise for closely related - CLI:
nucmer --maxmatch ref.fa query.fathendnadiff-- MUMmer4 pairwise - CLI:
anchorwave proali --ploidy 4-- WGD-aware sequence-level synteny alignment
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.
- 9d ago First seen · 456 lines · 237 tokens per session scan A 01f5edbe9699
bio-comparative-genomics-whole-genome-alignment is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 237 tokens to every session and 7,929 once invoked, about $0.0012 per session on Opus 5. A static security scan graded it A with 0 findings. It is 94% identical to bio-comparative-genomics-whole-genome-alignment, differing in 14 lines, and is treated as a copy.
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