EVEE MCP Server
Provides interpretable variant effect predictions for 4.2 million ClinVar variants using the EVEE API. Enables searching, comparing, and analyzing genetic variants with AI-generated mechanistic interpretations and disruption profiles.
README
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.
Recommended Servers
playwright-mcp
A Model Context Protocol server that enables LLMs to interact with web pages through structured accessibility snapshots without requiring vision models or screenshots.
Magic Component Platform (MCP)
An AI-powered tool that generates modern UI components from natural language descriptions, integrating with popular IDEs to streamline UI development workflow.
Audiense Insights MCP Server
Enables interaction with Audiense Insights accounts via the Model Context Protocol, facilitating the extraction and analysis of marketing insights and audience data including demographics, behavior, and influencer engagement.
VeyraX MCP
Single MCP tool to connect all your favorite tools: Gmail, Calendar and 40 more.
graphlit-mcp-server
The Model Context Protocol (MCP) Server enables integration between MCP clients and the Graphlit service. Ingest anything from Slack to Gmail to podcast feeds, in addition to web crawling, into a Graphlit project - and then retrieve relevant contents from the MCP client.
Kagi MCP Server
An MCP server that integrates Kagi search capabilities with Claude AI, enabling Claude to perform real-time web searches when answering questions that require up-to-date information.
E2B
Using MCP to run code via e2b.
Neon Database
MCP server for interacting with Neon Management API and databases
Exa Search
A Model Context Protocol (MCP) server lets AI assistants like Claude use the Exa AI Search API for web searches. This setup allows AI models to get real-time web information in a safe and controlled way.
Qdrant Server
This repository is an example of how to create a MCP server for Qdrant, a vector search engine.