| Name | evo2-mcp JSON |
| Version |
0.2.2
JSON |
| download |
| home_page | None |
| Summary | MCP server for generating, scoring and embedding genomic sequences using Evo 2 |
| upload_time | 2025-10-23 13:49:43 |
| maintainer | None |
| docs_url | None |
| author | Jules Kreuer |
| requires_python | >=3.12 |
| license | GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".
The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.
The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.
1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.
2. Conveying Modified Versions.
If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
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a) under this License, provided that you make a good faith effort to
ensure that, in the event an Application does not supply the
function or data, the facility still operates, and performs
whatever part of its purpose remains meaningful, or
b) under the GNU GPL, with none of the additional permissions of
this License applicable to that copy.
3. Object Code Incorporating Material from Library Header Files.
The object code form of an Application may incorporate material from
a header file that is part of the Library. You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
layouts and accessors, or small macros, inline functions and templates
(ten or fewer lines in length), you do both of the following:
a) Give prominent notice with each copy of the object code that the
Library is used in it and that the Library and its use are
covered by this License.
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document.
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You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
the following:
a) Give prominent notice with each copy of the Combined Work that
the Library is used in it and that the Library and its use are
covered by this License.
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c) For a Combined Work that displays copyright notices during
execution, include the copyright notice for the Library among
these notices, as well as a reference directing the user to the
copies of the GNU GPL and this license document.
d) Do one of the following:
0) Convey the Minimal Corresponding Source under the terms of this
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Corresponding Source.
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you use option 4d0, the Installation Information must accompany
the Minimal Corresponding Source and Corresponding Application
Code. If you use option 4d1, you must provide the Installation
Information in the manner specified by section 6 of the GNU GPL
for conveying Corresponding Source.)
5. Combined Libraries.
You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
choice, if you do both of the following:
a) Accompany the combined library with a copy of the same work based
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6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
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Library. |
| keywords |
bioinformatics
deep-learning
embeddings
evo2
genomics
mcp
model-context-protocol
sequence-generation
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# evo2-mcp
[](https://biocontext.ai/registry/not-a-feature/evo2-mcp)
[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/not-a-feature/evo2-mcp/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/evo2-mcp
The evo2-mcp server exposes [Evo 2](https://github.com/ArcInstitute/evo2) 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 or newer
1. **Install Evo2 dependencies**: See [Installation Guide][installation] for details.
```bash
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**:
```bash
pip install evo2-mcp
```
3. **Activate MCP Server**:
Add the following to your `mcp.json` configuration:
```json
{
"mcpServers": {
"evo2-mcp": {
"command": "python",
"args": ["-m", "evo2_mcp.main"]
}
}
}
```
For detailed installation instructions, see the [Installation Guide][installation].
## Usage
Once installed, the server can be accessed by any MCP-compatible client. For available tools and usage examples, see the [Tools Documentation][tools].
### 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][tools] for detailed API reference and examples.
## Documentation
- **[Installation Guide][installation]** - Detailed installation instructions
- **[Tools Reference][tools]** - Complete API documentation and usage examples
- **[Development Guide][development]** - Contributing and testing information
- **[Changelog][changelog]** - Version history and updates
You can also find this project on [BioContextAI](https://biocontext.ai/registry/not-a-feature/evo2-mcp), the community hub for biomedical MCP servers.
## Citation
If you use evo2-mcp in your research, please cite:
```bibtex
@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 = {0.2.2}
}
```
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](https://github.com/ArcInstitute/evo2/blob/main/evo2.jpg) from the [Evo 2 project](https://github.com/ArcInstitute/evo2), which is released under the [Apache 2.0 License](https://www.apache.org/licenses/LICENSE-2.0). It was modified using Google Gemini "Nanobana" and GIMP.
[installation]: https://evo2-mcp.readthedocs.io/en/latest/installation.html
[tools]: https://evo2-mcp.readthedocs.io/en/latest/tools.html
[development]: https://evo2-mcp.readthedocs.io/en/latest/development.html
[issue tracker]: https://github.com/not-a-feature/evo2-mcp/issues
[tests]: https://github.com/not-a-feature/evo2-mcp/actions/workflows/test.yaml
[documentation]: https://evo2-mcp.readthedocs.io
[changelog]: https://evo2-mcp.readthedocs.io/en/latest/changelog.html
[pypi]: https://pypi.org/project/evo2-mcp
Raw data
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"download_url": "https://files.pythonhosted.org/packages/76/78/f0f47023147e7f55e062e443835f87dbcc285364f2394a7b2b78a4155ad4/evo2_mcp-0.2.2.tar.gz",
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"description": "# evo2-mcp\n\n\n\n[](https://biocontext.ai/registry/not-a-feature/evo2-mcp)\n[![Tests][badge-tests]][tests]\n[![Documentation][badge-docs]][documentation]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/not-a-feature/evo2-mcp/test.yaml?branch=main\n[badge-docs]: https://img.shields.io/readthedocs/evo2-mcp\n\nThe evo2-mcp server exposes [Evo 2](https://github.com/ArcInstitute/evo2) 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.\n\n## Features\n\n- **Sequence Scoring**: Compute log probabilities for DNA sequences\n- **Sequence Embedding**: Extract learned representations from intermediate model layers\n- **Sequence Generation**: Generate novel DNA sequences with controlled sampling\n- **Variant Effect Prediction**: Score SNP mutations for variant prioritization\n- **Multiple Model Checkpoints**: Support for 7B, 40B, and 1B parameter models\n\n## Getting Started\n\n**Prerequisites**: Python 3.12 or newer\n\n1. **Install Evo2 dependencies**: See [Installation Guide][installation] for details.\n ```bash\n conda install -c nvidia cuda-nvcc cuda-cudart-dev\n conda install -c conda-forge transformer-engine-torch=2.3.0\n pip install flash-attn==2.8.0.post2 --no-build-isolation\n pip install evo2\n ```\n\n2. **Install evo2-mcp**:\n ```bash\n pip install evo2-mcp\n ```\n\n3. **Activate MCP Server**:\n Add the following to your `mcp.json` configuration:\n\n ```json\n {\n \"mcpServers\": {\n \"evo2-mcp\": {\n \"command\": \"python\",\n \"args\": [\"-m\", \"evo2_mcp.main\"]\n }\n }\n }\n ```\n\nFor detailed installation instructions, see the [Installation Guide][installation].\n\n## Usage\n\nOnce installed, the server can be accessed by any MCP-compatible client. For available tools and usage examples, see the [Tools Documentation][tools].\n\n### Available Tools\n\n- `score_sequence` - Evaluate DNA sequence likelihood\n- `embed_sequence` - Extract feature representations\n- `generate_sequence` - Generate novel DNA sequences\n- `score_snp` - Predict variant effects\n- `get_embedding_layers` - List available embedding layers\n- `list_available_checkpoints` - Show supported model checkpoints\n\nSee the [Tools Documentation][tools] for detailed API reference and examples.\n\n## Documentation\n\n- **[Installation Guide][installation]** - Detailed installation instructions\n- **[Tools Reference][tools]** - Complete API documentation and usage examples\n- **[Development Guide][development]** - Contributing and testing information\n- **[Changelog][changelog]** - Version history and updates\n\nYou can also find this project on [BioContextAI](https://biocontext.ai/registry/not-a-feature/evo2-mcp), the community hub for biomedical MCP servers.\n\n## Citation\n\nIf you use evo2-mcp in your research, please cite:\n\n```bibtex\n@software{evo2_mcp,\n author = {Kreuer, Jules},\n title = {evo2-mcp: MCP server for Evo 2 genomic sequence operations},\n year = {2025},\n url = {https://github.com/not-a-feature/evo2-mcp},\n version = {0.2.2}\n}\n```\n\nFor the underlying Evo 2 model, please also cite the original Evo 2 publication.\n\n## License and Attribution\n\nThe banner image in this repository is a modified version of the original [Evo 2 banner](https://github.com/ArcInstitute/evo2/blob/main/evo2.jpg) from the [Evo 2 project](https://github.com/ArcInstitute/evo2), which is released under the [Apache 2.0 License](https://www.apache.org/licenses/LICENSE-2.0). It was modified using Google Gemini \"Nanobana\" and GIMP.\n\n[installation]: https://evo2-mcp.readthedocs.io/en/latest/installation.html\n[tools]: https://evo2-mcp.readthedocs.io/en/latest/tools.html\n[development]: https://evo2-mcp.readthedocs.io/en/latest/development.html\n[issue tracker]: https://github.com/not-a-feature/evo2-mcp/issues\n[tests]: https://github.com/not-a-feature/evo2-mcp/actions/workflows/test.yaml\n[documentation]: https://evo2-mcp.readthedocs.io\n[changelog]: https://evo2-mcp.readthedocs.io/en/latest/changelog.html\n[pypi]: https://pypi.org/project/evo2-mcp\n",
"bugtrack_url": null,
"license": "GNU LESSER GENERAL PUBLIC LICENSE\n Version 3, 29 June 2007\n \n Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>\n Everyone is permitted to copy and distribute verbatim copies\n of this license document, but changing it is not allowed.\n \n \n This version of the GNU Lesser General Public License incorporates\n the terms and conditions of version 3 of the GNU General Public\n License, supplemented by the additional permissions listed below.\n \n 0. Additional Definitions.\n \n As used herein, \"this License\" refers to version 3 of the GNU Lesser\n General Public License, and the \"GNU GPL\" refers to version 3 of the GNU\n General Public License.\n \n \"The Library\" refers to a covered work governed by this License,\n other than an Application or a Combined Work as defined below.\n \n An \"Application\" is any work that makes use of an interface provided\n by the Library, but which is not otherwise based on the Library.\n Defining a subclass of a class defined by the Library is deemed a mode\n of using an interface provided by the Library.\n \n A \"Combined Work\" is a work produced by combining or linking an\n Application with the Library. The particular version of the Library\n with which the Combined Work was made is also called the \"Linked\n Version\".\n \n The \"Minimal Corresponding Source\" for a Combined Work means the\n Corresponding Source for the Combined Work, excluding any source code\n for portions of the Combined Work that, considered in isolation, are\n based on the Application, and not on the Linked Version.\n \n The \"Corresponding Application Code\" for a Combined Work means the\n object code and/or source code for the Application, including any data\n and utility programs needed for reproducing the Combined Work from the\n Application, but excluding the System Libraries of the Combined Work.\n \n 1. Exception to Section 3 of the GNU GPL.\n \n You may convey a covered work under sections 3 and 4 of this License\n without being bound by section 3 of the GNU GPL.\n \n 2. Conveying Modified Versions.\n \n If you modify a copy of the Library, and, in your modifications, a\n facility refers to a function or data to be supplied by an Application\n that uses the facility (other than as an argument passed when the\n facility is invoked), then you may convey a copy of the modified\n version:\n \n a) under this License, provided that you make a good faith effort to\n ensure that, in the event an Application does not supply the\n function or data, the facility still operates, and performs\n whatever part of its purpose remains meaningful, or\n \n b) under the GNU GPL, with none of the additional permissions of\n this License applicable to that copy.\n \n 3. Object Code Incorporating Material from Library Header Files.\n \n The object code form of an Application may incorporate material from\n a header file that is part of the Library. You may convey such object\n code under terms of your choice, provided that, if the incorporated\n material is not limited to numerical parameters, data structure\n layouts and accessors, or small macros, inline functions and templates\n (ten or fewer lines in length), you do both of the following:\n \n a) Give prominent notice with each copy of the object code that the\n Library is used in it and that the Library and its use are\n covered by this License.\n \n b) Accompany the object code with a copy of the GNU GPL and this license\n document.\n \n 4. Combined Works.\n \n You may convey a Combined Work under terms of your choice that,\n taken together, effectively do not restrict modification of the\n portions of the Library contained in the Combined Work and reverse\n engineering for debugging such modifications, if you also do each of\n the following:\n \n a) Give prominent notice with each copy of the Combined Work that\n the Library is used in it and that the Library and its use are\n covered by this License.\n \n b) Accompany the Combined Work with a copy of the GNU GPL and this license\n document.\n \n c) For a Combined Work that displays copyright notices during\n execution, include the copyright notice for the Library among\n these notices, as well as a reference directing the user to the\n copies of the GNU GPL and this license document.\n \n d) Do one of the following:\n \n 0) Convey the Minimal Corresponding Source under the terms of this\n License, and the Corresponding Application Code in a form\n suitable for, and under terms that permit, the user to\n recombine or relink the Application with a modified version of\n the Linked Version to produce a modified Combined Work, in the\n manner specified by section 6 of the GNU GPL for conveying\n Corresponding Source.\n \n 1) Use a suitable shared library mechanism for linking with the\n Library. A suitable mechanism is one that (a) uses at run time\n a copy of the Library already present on the user's computer\n system, and (b) will operate properly with a modified version\n of the Library that is interface-compatible with the Linked\n Version.\n \n e) Provide Installation Information, but only if you would otherwise\n be required to provide such information under section 6 of the\n GNU GPL, and only to the extent that such information is\n necessary to install and execute a modified version of the\n Combined Work produced by recombining or relinking the\n Application with a modified version of the Linked Version. (If\n you use option 4d0, the Installation Information must accompany\n the Minimal Corresponding Source and Corresponding Application\n Code. If you use option 4d1, you must provide the Installation\n Information in the manner specified by section 6 of the GNU GPL\n for conveying Corresponding Source.)\n \n 5. Combined Libraries.\n \n You may place library facilities that are a work based on the\n Library side by side in a single library together with other library\n facilities that are not Applications and are not covered by this\n License, and convey such a combined library under terms of your\n choice, if you do both of the following:\n \n a) Accompany the combined library with a copy of the same work based\n on the Library, uncombined with any other library facilities,\n conveyed under the terms of this License.\n \n b) Give prominent notice with the combined library that part of it\n is a work based on the Library, and explaining where to find the\n accompanying uncombined form of the same work.\n \n 6. Revised Versions of the GNU Lesser General Public License.\n \n The Free Software Foundation may publish revised and/or new versions\n of the GNU Lesser General Public License from time to time. Such new\n versions will be similar in spirit to the present version, but may\n differ in detail to address new problems or concerns.\n \n Each version is given a distinguishing version number. If the\n Library as you received it specifies that a certain numbered version\n of the GNU Lesser General Public License \"or any later version\"\n applies to it, you have the option of following the terms and\n conditions either of that published version or of any later version\n published by the Free Software Foundation. If the Library as you\n received it does not specify a version number of the GNU Lesser\n General Public License, you may choose any version of the GNU Lesser\n General Public License ever published by the Free Software Foundation.\n \n If the Library as you received it specifies that a proxy can decide\n whether future versions of the GNU Lesser General Public License shall\n apply, that proxy's public statement of acceptance of any version is\n permanent authorization for you to choose that version for the\n Library.",
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