Evo2 MCP

MCP server for generating, scoring and embedding genomic sequences using Evo 2

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evo2-mcp#

evo2-mcp banner

BioContextAI - Registry Tests Documentation

The evo2-mcp server exposes Evo 2 as a Model Context Protocol (MCP) server, providing tools for genomic sequence analysis. Any MCP-compatible client can use these tools to score, embed, and generate DNA sequences.

Features#

  • Sequence Scoring: Compute log probabilities for DNA sequences
  • Sequence Embedding: Extract learned representations from intermediate model layers
  • Sequence Generation: Generate novel DNA sequences with controlled sampling
  • Variant Effect Prediction: Score SNP mutations for variant prioritization
  • Multiple Model Checkpoints: Support for 7B, 40B, and 1B parameter models

Getting Started#

Prerequisites: Python 3.12

  1. Install Evo2 dependencies: See Installation Guide for details.
    conda install -c nvidia cuda-nvcc cuda-cudart-dev
    conda install -c conda-forge transformer-engine-torch=2.3.0
    pip install flash-attn==2.8.0.post2 --no-build-isolation
    pip install evo2
  2. Install evo2-mcp:
    pip install evo2-mcp
  3. Activate MCP Server: Add the following to your mcp.json configuration:
    {
    "mcpServers": {
    "evo2-mcp": {
    "command": "python",
    "args": ["-m", "evo2_mcp.main"]
    }
    }
    }

For detailed installation instructions, see the Installation Guide.

Usage#

Once installed, the server can be accessed by any MCP-compatible client. For available tools and usage examples, see the Tools Documentation.

Available Tools#

  • score_sequence - Evaluate DNA sequence likelihood
  • embed_sequence - Extract feature representations
  • generate_sequence - Generate novel DNA sequences
  • score_snp - Predict variant effects
  • get_embedding_layers - List available embedding layers
  • list_available_checkpoints - Show supported model checkpoints

See the Tools Documentation for detailed API reference and examples.

Documentation#

You can also find this project on BioContextAI, the community hub for biomedical MCP servers.

Citation#

If you use evo2-mcp in your research, please cite:

@software{evo2_mcp, author = {Kreuer, Jules}, title = {evo2-mcp: MCP server for Evo 2 genomic sequence operations}, year = {2025}, url = {https://github.com/not-a-feature/evo2-mcp}, version = {0.2.3} }

For the underlying Evo 2 model, please also cite the original Evo 2 publication.

License and Attribution#

The banner image in this repository is a modified version of the original Evo 2 banner from the Evo 2 project, which is released under the Apache 2.0 License. It was modified using Google Gemini “Nanobana” and GIMP.

Getting Started

Tools & Usage

Development

Contents

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