MMseqs2
Very fast sequence search and clustering, the MSA engine behind ColabFold.
Developer: Steinegger and Söding labs
Overview
- Developer
- Steinegger and Söding labs
- Category
- Data and structure resources
- Commercial rights
- Commercial OK
- Commercial cost
- Free commercially
- Compute
- CPU
- Open weights
- Yes
- Last verified
Capabilities
Sequence search and clustering at scale. Input: query and target FASTA/databases; output: homology hits, clusters and MSA profiles in minutes where BLAST takes days - the MSA engine behind ColabFold.
When to use it
Use to build your own MSAs or cluster large sequence sets locally instead of hitting public servers. Needs lots of RAM and disk for big databases.
Input / Output
- Input
- query and target FASTA/databases
- Output
- homology hits, clusters and MSA profiles in minutes where BLAST takes days - the MSA engine behind ColabFold
Compute
Commercial Licensing
Commercial rights — may a company use it?
Commercial use OKLicence as writtenMIT License
LICENSE.md in the repo is 'The MIT License (MIT)'.
The licence read at the source allows use by a company. Attribution or copyleft conditions may still apply — read the note.
Commercial cost — is commercial use free of charge?
Free for commercial useNothing to pay: the licence read at the source grants commercial use with no fee, and the code and weights are public downloads. You still pay for your own compute.
Price and rights are separate: this panel is about money, the panel above is about permission.
- Commercial OK ≠ Free of charge. A tool can be licensed for company use and still need a paid licence for a dependency (BindCraft → PyRosetta).
- Free download ≠ Commercially licensed. Weights you can download at no cost may still forbid commercial use (AlphaFold 3).
- Unverified ≠ Commercially permitted. If no published statement settles it, treat it as unknown — not as a yes.
- Every component counts. Each status considers the code licence, the model-weights terms, required dependencies and any terms of use.
Model Weights
Open weights. A separate weights licence is Not documented as its own field; where weights carry different terms from the code, that is stated in the licence explanation above.
Dependencies
Not documented as a separate field. Any dependency that affects commercial use (for example a paid PyRosetta licence) is named in the licence and cost explanations above.
Official References
- Official site / repo
- github.com/soedinglab/MMseqs2
From the makers of FoldScout
From AI Design to Wet-Lab Validation
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Get told when a licence changes
Licences on these tools do change. One short email when a status flips or a tool is added. No other use of your address.