bio-comparative-genomics-gene-family-evolution
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 annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contrac
npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-family-evolution --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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 (Liu 2016), 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 **"Which gene families expanded or
- Version Compatibility
- Algorithmic Taxonomy
- Decision Tree by Experimental Scenario
- Per-Tool Failure Modes
- Annotation heterogeneity inflating expansions / contractions
- Assembly fragmentation creating false contractions
- CAFE5 lambda non-convergence
- Gamma rate-category misinterpretation
- Multiple-testing across many families
- Tree non-ultrametric / negative branches
- Outlier-family-driven lambda estimate
- Convergent gene-family-rate shifts not captured
- CAFE5 vs ALE for HGT-affected family
- Family classification (single-copy / multi-copy) affecting interpretation
python3 <<'PY'
Output format: Description family_id Species1 Species2 ... (counts per species)
Rscript -e "
tree <- read.tree('SpeciesTree_rooted.txt')
tree_ultra <- chronos(tree)
cafe5 \
error model file, use `-eerror.txt` (CAFE5 concatenates the flag and argument).
Verify with `cafe5 --help`.
cafe_output/Base_results.txt Per-family results
cafe_output/Base_clade_results.txt Per-clade lambdaWhat does the bio-comparative-genomics-gene-family-evolution skill do?
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 annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contrac
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-family-evolution --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.