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MCP server · AI

Evo2 MCP

by · github.com/not-a-feature/evo2-mcp

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

Unclaimed LGPL-3.0 last commit 6 months ago ai
InstallView source
54Fair

Scored 5 days ago · breakdown

About Evo2 MCP

Evo2 MCP is an MCP server published by not-a-feature in the AI category: mCP server for generating, scoring and embedding genomic sequences using Evo 2.

The repository has 2 stars and 0 forks, with the last commit 6 months ago. Six months or more without a commit doesn't mean the server is broken, but check the open issues before depending on it in production.

Install

From source
git clone https://github.com/not-a-feature/evo2-mcp

This server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.

Tools (6)

embed_sequenceExtract feature representations

Parameters not published.

generate_sequenceGenerate novel DNA sequences

Parameters not published.

get_embedding_layersList available embedding layers

Parameters not published.

list_available_checkpointsShow supported model checkpoints

Parameters not published.

score_sequenceEvaluate DNA sequence likelihood

Parameters not published.

score_snpPredict variant effects

Parameters not published.

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Security checks

Static checks derived from the repository 5 days ago. Heuristics on the source, not an audit.

  • ✓README presentThe repository ships documentation.
  • ✓License declaredUsable under a stated license.
  • ✓Tests presentA test suite exists in the repository.
  • !Dependencies pinnedNo lockfile. Installs can pull different code over time.
  • ✓No dynamic code executionSource scan found no eval, dynamic Function, or shell execution.
  • !Scoped permissionsDoesn't declare a permission scope. Assume it can do anything its process can.

Releases

v0.2.3v0.2.3 - pin fastmcp versin · 13 Apr 2026Full Changelog: https://github.com/not-a-feature/evo2-mcp/compare/v0.2.2...v0.2.3
v0.2.2v0.2.2 - improved documentation · 23 Oct 2025Full Changelog: https://github.com/not-a-feature/evo2-mcp/compare/v0.2.1...v0.2.2
v0.2.1v0.2.1 - improved tool description · 20 Oct 2025Full Changelog: https://github.com/not-a-feature/evo2-mcp/compare/v0.2.0...v0.2.1
v0.2.0v0.2.0 - added get_embedding_layers and improved docs · 20 Oct 2025Full Changelog: https://github.com/not-a-feature/evo2-mcp/compare/v0.1.0...v0.2.0
v0.1.0v0.1.0 - initial release · 19 Oct 2025Full Changelog: https://github.com/not-a-feature/evo2-mcp/commits/v0.1.0

README

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.

README fetched from the repository 5 days ago. The original is authoritative.

Questions

About Evo2 MCP

How do I install Evo2 MCP?

No package has been published for this server, so install it from source: clone the repository and follow its README.

Is Evo2 MCP safe to use with an AI agent?

Its trust score is 54 out of 100 (fair). It passes 4 of the 6 static security checks run so far; the failures are listed above. It has no ConduID identity yet, so agent calls to it are not receipted.

Is Evo2 MCP still maintained?

The last commit was 6 months ago. That's long enough that you should check whether the maintainer is responding to issues before depending on it.