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 GPTomics/bioSkills --skill gene-family-evolutiongit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/gene-family-evolution)<a href="https://agentmods.dev/skills/gptomics/bioskills/gene-family-evolution"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gene-family-evolution/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/gptomics/bioskills/gene-family-evolution"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gene-family-evolution.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 | $0.00189 | $0.06603 |
| Opus 5 | $0.00095 | $0.03302 |
| Sonnet 5 | $0.00038 | $0.01321 |
| Haiku 4.5 | $0.00019 | $0.00660 |
Grade A, and why
bio-comparative-genomics-gene-family-evolution scanned grade A with 1 finding 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 7d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget http://www.iro.umontreal.ca/~csuros/gene_content/count.tar.gz Copies of this mod
1 near-identical copy found in the catalogue:
- bio-comparative-genomics-gene-family-evolution — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 441 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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
"Which gene families expanded or contracted in which lineages?" -> Birth-death models on phylogeny (Hahn 2005; Csurös 2010) treat each orthogroup's per-species count as evolving under a stochastic birth-death process; lineage-specific rate shifts are detected as departures from a global rate. Annotation heterogeneity is the single largest confounder: different annotation pipelines predict different numbers of genes per family, producing apparent lineage-specific expansions that are artifacts of annotation choice (Tonkin-Hill 2020 demonstrated this for bacterial pangenomes). Consistent annotation + BUSCO/Compleasm completeness filtering are mandatory before any birth-death model interpretation. CAFE5 (Mendes et al 2020 Bioinformatics 36:5516) replaces older CAFE versions with gamma-distributed rate categories for more biologically realistic modeling.
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.
- 7d ago First seen · 441 lines · 189 tokens per session scan A 52d68664c754
bio-comparative-genomics-gene-family-evolution is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 189 tokens to every session and 6,603 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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