bio-comparative-genomics-whole-genome-duplication SKILL.md skillA
bio-comparative-genomics-whole-genome-duplication from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
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- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
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skills/bioskills/bio-comparative-genomics-whole-genome-duplication/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- 662
- License
- MIT
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication@sha256:4ee13807bc3aa07aThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_d2an5c7jb3qeqx27)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_d2an5c7jb3qeqx27 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-comparative-genomics-whole-genome-duplication GET https://markdownregistry.com/api/v1/blob/4ee13807bc3aa07a36decabe614a5583038ee3da2750de7beca64fcdbd6f5d52
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.