Method

MMseqs2

MMseqs2 searches and clusters large protein and nucleotide sequence collections.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

How it worksMMseqs2 workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

At a glance

Model type

Sequence search and clustering software

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Inputs

Protein or nucleotide query sequences and a reference database, or sequences to cluster.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Outputs

Sequence hits, alignments, clusters or configured taxonomic assignments.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

How it works

MMseqs2 searches and clusters large protein and nucleotide sequence collections. Sequence/profile search and clustering software with CPU and selected GPU execution paths. The documented inputs are protein or nucleotide query sequences and a reference database, or sequences to cluster. The output consists of sequence hits, alignments, clusters or configured taxonomic assignments.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Versions and reproducibility

MMseqs2 software release and database build must both be pinned; GPU capability differs by build. Database/query scale and implementation limits, not a neural token window.

Sources

soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Strengths and limitations

Strengths supported by sources

Provides reusable search and clustering procedures suitable as homology-based comparators.
Sources
soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Limitations and conditions

Hardware paths, sensitivity settings and reference database versions affect an evaluation. A sequence-similarity hit is not itself a validated functional measurement.
Sources
soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-mmseqs2

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Sequence search and clustering software Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Architecture	Sequence/profile search and clustering software with CPU and selected GPU execution paths. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Inputs	Protein or nucleotide query sequences and a reference database, or sequences to cluster. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Outputs	Sequence hits, alignments, clusters or configured taxonomic assignments. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Parameters	Inapplicable as a neural parameter count; search and clustering settings apply. · Not applicable Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Known versions	MMseqs2 software release and database build must both be pinned; GPU capability differs by build. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Training data	Reference sequence/profile databases rather than neural pretraining. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Context limits	Database/query scale and implementation limits, not a neural token window. Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Weights licence	Inapplicable: no neural checkpoint in the core search/clustering method. · Not applicable Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Access	Official project documentation and implementation: https://github.com/soedinglab/MMseqs2 Sources soedinglab/MMseqs2: README.md · README.md: opening, Publications, Installation and user-guide pointers
Code licence	MIT Sources soedinglab/MMseqs2: LICENSE.md · LICENSE.md: licence text
Assumptions	Not extracted or verified for this record.

Applicable tests and references

Applicability is distinct from a completed evaluation.

CAFA · Proposed association

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Sequence collection","Configured search or clustering","Sequence relationships","Hits or clusters"] Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title MMseqs2 workflow Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Sequence search and clustering software Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Sequence/profile search and clustering software with CPU and selected GPU execution paths. Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Access Official project documentation and implementation: https://github.com/soedinglab/MMseqs2 Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Code licence MIT Individual claims	soedinglab/MMseqs2: LICENSE.md Original source ↗ LICENSE.md: licence text Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.11.value` Source artifact SHA-256: `adc3ea1f2f5096d2464460495e12a65a94f466edb9ccca50d1f25844ca83792a` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Inputs Protein or nucleotide query sequences and a reference database, or sequences to cluster. Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Outputs Sequence hits, alignments, clusters or configured taxonomic assignments. Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Parameters Inapplicable as a neural parameter count; search and clustering settings apply. Individual claims	soedinglab/MMseqs2: README.md Original source ↗ README.md: opening, Publications, Installation and user-guide pointers Version: d401e78c2d18a822cdb1527d7464a043f6035a15 Retrieved: 2026-09-16T19:46:20.231620+00:00	inapplicable automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: discovered

3 source records and release history

soedinglab/MMseqs2 official source · Original source · d401e78c2d18a822cdb1527d7464a043f6035a15
soedinglab/MMseqs2: README.md · Original source · d401e78c2d18a822cdb1527d7464a043f6035a15
soedinglab/MMseqs2: LICENSE.md · Original source · d401e78c2d18a822cdb1527d7464a043f6035a15

Download this release

Technical metadata and extraction receipts

Stable ID: discovery-model-mmseqs2

areas: protein-function
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-cafa
entity level: method
reported name: MMseqs2
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-81e51077d7d3352a6de4; source locator: README.md: opening, Publications, Installation and user-guide pointers; ambiguities: None recorded

Related records

applicable to: CAFA
model: Protein homology transfer

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