bio-comparative-genomics-gene-family-evolution SKILL.md skillA
bio-comparative-genomics-gene-family-evolution 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-gene-family-evolution@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-comparative-genomics-gene-family-evolution/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- License
- MIT
Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from…
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: CAFE5 5.1.0+ (Mendes et al 2020 Bioinformatics 36(22-23):5516-5518), Count 11.0319+ (Csurös 2010 Bioinformatics 26:1910), BadiRate 1.35+ (Librado 2012 Bioinformatics 28:279), DupliPHY-Family (Ames et al 2012), CAFExp (legacy CAFE 4.2 -- DEPRECATED; use CAFE5), OrthoFinder 3.0+ for HOG input, R 4.4+, mclust 6.1+, phytools 2.3+, ETE4 4.1.0+ for tree manipulation. ALE/GeneRax/AleRax in companion skill [[gene-tree-species-tree-reconciliation]].
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `cafe5 --help`; `Count.exe` (Java); `badirate --help`
- R: `packageVersion('phytools')`
- Python: `pip show ete4`
If code throws `CAFE5: lambda did not converge`, `Count negative branch length`, `BadiRate gamma not initialized`, the most common causes are: (1) annotation heterogeneity inflating family sizes, (2) saturated families (CAFE5 needs reasonable rate variation), (3) negative branch lengths in input tree (Count requires ultrametric). Pre-process: filter OG matrix to families present in >= 50% of species; resolve polytomies; ultrametricize tree.
# Gene Family Evolution
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-gene-family-evolution@sha256:4c76fb0300910d09The 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_atuoclqhypzp6n6l)
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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_atuoclqhypzp6n6l GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-comparative-genomics-gene-family-evolution GET https://markdownregistry.com/api/v1/blob/4c76fb0300910d09c12607a75f49e2353b470a2e31306e161f12fa0f75335983
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.