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-duplicationgit 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-duplication)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication/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-duplication"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication.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 | $0.00221 | $0.07998 |
| Opus 5 | $0.00111 | $0.03999 |
| Sonnet 5 | $0.00044 | $0.01600 |
| Haiku 4.5 | $0.00022 | $0.00800 |
Grade A, and why
bio-comparative-genomics-whole-genome-duplication 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
95% identical to bio-comparative-genomics-whole-genome-duplication — 12 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 — 460 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: wgd v2.0.31+ (heche-psb/wgd; Chen et al 2024 Bioinformatics 40:btae272), KsRates 1.1.3+ (VIB-PSB/ksrates; Sensalari 2022 Bioinformatics 38:530), DupGen_finder (Qiao 2019 Genome Biol 20:38), MAPS 1.0 (Li 2018), POInT (Conant lab), SLEDGe (bioRxiv 2024.01.17.574559), Whale.jl 2.0+, ksrates pip 1.1+, MCScanX 1.0+, PAML 4.10+ (yn00/codeml for Ks), BLAT 36+, DIAMOND 2.1+, R 4.4+, mclust 6.1+ (for mixture models). Python 3.10+ required for wgd v2.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
wgd --version;ksrates --version;wgd ksd --help - Python:
pip show wgd ksrates - R:
packageVersion('mclust')
If code throws wgd ksd: cannot find PAML output, KsRates: insufficient sister species, MAPS: missing tree, these tools have specific input expectations: wgd needs codon-aware MAFFT/MUSCLE alignment; KsRates needs configured config_ksrates.txt; MAPS needs nucleotide tree. The deprecated arzwa/wgd v1 is replaced by heche-psb/wgd v2.
Whole Genome Duplication Analysis
"Are there WGD events in this lineage and when did they occur?" -> WGD detection combines Ks distributions (synonymous-substitution rates between gene paralog pairs, showing peaks at past polyploidy events) and synteny block analysis (parallel collinear blocks within a genome). Modern best practice uses wgd v2 (Chen et al 2024 Bioinformatics 40:btae272) as an integrated pipeline. KsRates (Sensalari 2022 Bioinformatics 38:530) is mandatory for cross-lineage comparison because substitution rates vary across the tree -- ignoring this places WGDs incorrectly relative to speciation events. The fundamental tradeoff: Ks plot peaks are visually obvious but biologically ambiguous between (1) small-scale tandem duplications, (2) segmental duplications, and (3) true WGD; combining Ks with synteny anchors disambiguates these.
- CLI:
wgd dmdandwgd ksd-- paranome construction + Ks distribution - CLI:
wgd syn-- synteny-anchored WGD signal extraction - CLI:
ksrates initthenksrates wgd-paralogs ortho-- substitution-rate-corrected positioning - CLI:
MCScanX -hthendupgen_finder-- duplication-class assignment - CLI:
mapsR-- gene-tree-based WGD phylogenetic placement
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 · 460 lines · 221 tokens per session scan A 4ee13807bc3a
bio-comparative-genomics-whole-genome-duplication is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 221 tokens to every session and 7,998 once invoked, about $0.0011 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-comparative-genomics-whole-genome-duplication, differing in 12 lines, and is treated as a copy.
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