Skip to content


Repository files navigation

App and Server for MMseqs2, Foldseek and ColabFold

MMseqs2 and Foldseek are software suites to search and annotate huge sequence and structure sets. We built a graphical interface for interactive data exploration. Check out a live instance for MMseqs2 and for Foldseek. Additionally, this codebase holds the API server for ColabFold.

The application runs either:

  • on your server through docker-compose, where it can make your sequence, profile or structure databases easily accessible over the web
  • on your workstation as a cross-platform desktop application with the help of Electron

Desktop App

Head over to the release page and download the latest version. We support Linux, macOS and Windows.

Adding a search database

Once the app is installed, open the Settings panel. There you can add either sequence databases in FASTA format, such as our Uniclust databases or profile databases in Stockholm format, such as the PFAM.

Web app quick start with docker-compose

Make sure you have docker, docker-compose and git installed on your server. To start the MMseqs2/Foldseek web server execute the following commands. Afterwards you can navigate to http://localhost:8877 to access the interface.

# clone the repository
git clone

# navigate to our docker recipes
cd MMseqs2-App/docker-compose

# (optional) edit the APP entry in the .env file to choose between mmseqs and foldseek

# list available databases
docker-compose run db-setup

# download PDB
docker-compose run db-setup PDB

# start the server with docker-compose
docker-compose up

By default, the server will start on port 8877. You can edit the .env file in the docker-compose directory to change this port.

Head over to the docker-compose readme for more details on running your own server, including how to add your own sequence, profile or structure databases. Take a look at the API documentation to learn how to talk to the server backend.

Building the desktop app

You need to have git, go (>=1.18), node, npm and make installed on your system.

Afterwards run the following commands, and the apps will appear in the build folder.

# clone the repository
git clone
cd MMseqs2-App

# install all dependencies
npm install

# build the app for all platforms, choose either mmseqs or foldseek
FRONTEND_APP=mmseqs npm run electron:build