EVEE MCP Server
MCP server for the EVEE (Evo Variant Effect Explorer) API — interpretable variant effect prediction from Evo 2 genomic foundation model embeddings.
EVEE provides pre-computed pathogenicity predictions, disruption profiles, and AI-generated mechanistic interpretations for 4.2 million ClinVar variants. See Pearce et al. (2026) for the full paper.
Tools
| Tool | Description |
|---|---|
search_variants | Autocomplete-style lookup (≤6 matches) for a gene symbol, rsID, or ClinVar variation ID; useful for finding candidate variant IDs, not an exhaustive gene-wide ranking |
get_variant | Clinical summary, EVEE-derived effect outputs, database comparison scores when present, and the AI-generated mechanistic interpretation (auto-triggers on-demand generation when not yet stored) |
wait_for_variant_analysis | Poll EVEE's on-demand interpretation generation until it completes or times out |
compare_variants | Side-by-side summary (up to 10 variants in one call) — clinical label, pathogenicity, top-1 disruption, HGVS, deep link |
get_variant_disruptions | Top biological annotation disruptions ranked by magnitude, optionally scoped to a category — explains why a variant is predicted pathogenic or benign |
get_variant_annotations | Full annotation probe values (325 annotations across 13 categories), optionally filtered by category |
Annotation categories
amino_acid, atacseq, ccre, chipseq, chromhmm, elm, fstack, protein_feature, interpro, genomic_feature, ptm, region, secondary_structure
Skill
A Claude Code skill lives at .claude/skills/evee/SKILL.md. Agents that load it get ~120 lines of guidance on how to use the tools effectively — workflow steps, reliability caveats by variant class, and gotchas (0-based coords, indel VCF anchoring, case-sensitivity).
Usage
Requires Python 3.10+ and uv.
git clone git@github.com:goodfire-ai/evee-mcp.git
cd evee-mcp
uv sync
Claude Code
The repo ships a .mcp.json; opening the directory triggers the permission prompt:
claude
Claude Desktop
Add to claude_desktop_config.json:
{
"mcpServers": {
"evee": {
"command": "uv",
"args": ["run", "--directory", "/absolute/path/to/evee-mcp", "python3", "server.py"]
}
}
}
Example
Is the FBN1 variant rs1597537935 pathogenic, and why?
The agent searches, fetches the clinical summary with the AI-generated mechanistic interpretation, and pulls out the top disruption evidence.