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-synteny-analysisgit 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-synteny-analysis)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-comparative-genomics-synteny-analysis"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-synteny-analysis/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-synteny-analysis"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-synteny-analysis.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 | $0.00192 | $0.09006 |
| Opus 5 | $0.00096 | $0.04503 |
| Sonnet 5 | $0.00038 | $0.01801 |
| Haiku 4.5 | $0.00019 | $0.00901 |
Grade A, and why
bio-comparative-genomics-synteny-analysis 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
97% identical to bio-comparative-genomics-synteny-analysis — 36 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 — 486 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: MCScanX 1.0+ (wyp1125/MCScanX commit 2020+), JCVI 1.4.21+ (Python port of MCScan), GENESPACE 1.4.0+ (Lovell 2022 eLife 11:e78526), SyRI 1.7.1+ (Goel 2019 Genome Biol 20:277), plotsr 1.1.1+, AnchorWave 1.2.5+ (Song 2022 PNAS 119:e2113075119), i-ADHoRe 3.0.01+, SynNet (Zhao 2017 Plant Cell 29:1278), ntSynt 1.0.4+ (2024), minimap2 2.28+, MUMmer 4.0.0+, OrthoFinder 3.0+, R 4.4+. plotsr requires pysam 0.22+ and seaborn 0.13+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
MCScanX -h;syri --version;python3 -m jcvi.compara.catalog ortholog --help - R:
packageVersion('GENESPACE');?run_genespace - Python:
pip show jcvi
If code throws MCScanX: argument bad format, syri: input alignment file missing required columns, or GENESPACE: GFF parse error, these tools have brittle input parsing: MCScanX requires 4-column species_chr gene start end BED (non-standard), JCVI expects 4-column simple BED, GENESPACE requires GFF3 with gene feature type. Pre-process with jcvi.formats.gff bed or custom AWK.
Synteny Analysis
"Compare genome architecture between these species" -> Detect conserved gene order (synteny) and infer rearrangement history. Synteny is NOT the same as collinearity: synteny is "genes on same chromosome", collinearity is "same order on same chromosome" (modern usage often conflates them). The choice of tool depends on whether the question is gene-level co-linearity (MCScanX, JCVI), whole-genome structural rearrangements (SyRI, AnchorWave), multi-genome macrosynteny (GENESPACE, ntSynt), or synteny-aware orthology (GENESPACE, ProteinOrtho-synteny). Repeat-masking quality is the dominant determinant of result reliability -- unmasked TEs produce ~100x more false anchor pairs than real syntenic anchors.
- CLI:
MCScanXfor collinear gene blocks via dynamic programming - CLI:
python3 -m jcvi.compara.catalog ortholog A Bfor JCVI/MCScan Python pipeline - R:
run_genespace()(Lovell 2022) for orthology-anchored riparian plots + pan-gene tracks - CLI:
syrifor inversion / translocation / duplication detection - CLI:
anchorwave proalifor sequence-level WGD-aware synteny
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 · 486 lines · 192 tokens per session scan A 2e6336d61094
bio-comparative-genomics-synteny-analysis is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 192 tokens to every session and 9,006 once invoked, about $0.0010 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to bio-comparative-genomics-synteny-analysis, differing in 36 lines, and is treated as a copy.
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