Model type
Profile-HMM sequence search software
Method
HH-suite
HH-suite searches for remote protein relationships using profile hidden Markov models.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageHow it worksHH-suite workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageAt a glance
Inputs
Protein sequence or alignment/profile and a selected reference profile database.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageOutputs
Homolog hits, alignments and related search scores.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageSource 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
How it works
HH-suite searches for remote protein relationships using profile hidden Markov models. Pairwise profile-HMM alignment with iterative homolog search utilities such as HHblits. The documented inputs are protein sequence or alignment/profile and a selected reference profile database. The output consists of homolog hits, alignments and related search scores.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageVersions and reproducibility
HH-suite3; README includes v3.3.0 binaries. Query/alignment size and database settings, not a learned token context.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and UsageStrengths and limitations
Strengths supported by sources
- Can search at the profile level and construct alignments of homologous sequences.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage
Limitations and conditions
- Search results depend on database coverage and iteration/settings. Profile similarity is evidence of sequence relationships rather than a direct functional assay.
Sources
soedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage
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-hh-suiteSpecifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Profile-HMM sequence search softwareSourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Architecture | Pairwise profile-HMM alignment with iterative homolog search utilities such as HHblits.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Inputs | Protein sequence or alignment/profile and a selected reference profile database.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Outputs | Homolog hits, alignments and related search scores.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Parameters | Profile probabilities and search settings; not a fixed neural parameter count.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Known versions | HH-suite3; README includes v3.3.0 binaries.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Training data | Profiles/reference databases rather than neural pretraining; examples include Uniclust30, BFD and PDB70.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Training cutoff | Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicableSourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Context limits | Query/alignment size and database settings, not a learned token context.Sourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Weights licence | Inapplicable: reference profiles/databases are the relevant artifacts. · Not applicableSourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Access | Official project documentation and implementation: https://github.com/soedinglab/hh-suiteSourcessoedinglab/hh-suite: README.md · README.md: opening, Available Databases and Usage |
| Code licence | GPL-3.0; inspect the pinned licence and any file-specific terms.Sourcessoedinglab/hh-suite: LICENSE · LICENSE: 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
| 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/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Query sequence or alignment","Profile HMM","Reference profile search","Homologs and alignment"] Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title HH-suite workflow Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Profile-HMM sequence search software Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Pairwise profile-HMM alignment with iterative homolog search utilities such as HHblits. Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Access Official project documentation and implementation: https://github.com/soedinglab/hh-suite Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Code licence GPL-3.0; inspect the pinned licence and any file-specific terms. Individual claims | soedinglab/hh-suite: LICENSE LICENSE: licence text Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Inputs Protein sequence or alignment/profile and a selected reference profile database. Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Outputs Homolog hits, alignments and related search scores. Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Parameters Profile probabilities and search settings; not a fixed neural parameter count. Individual claims | soedinglab/hh-suite: README.md README.md: opening, Available Databases and Usage Version: 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b | source checked automated source review · 2026-09-16 Audit detailsInspected 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: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
3 source records and release history
- soedinglab/hh-suite official source · Original source · 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b
- soedinglab/hh-suite: README.md · Original source · 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b
- soedinglab/hh-suite: LICENSE · Original source · 43095e46ada4ec2a8a47d47ef5ad7e38b1429f7b
Technical metadata and extraction receipts
Stable ID: discovery-model-hh-suite
- 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
- HH-suite
- 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-863f6c2e6e18152c2f8b; source locator: README.md: opening, Available Databases and Usage; ambiguities: None recorded
Related records
- applicable to: CAFA
- model: Profile-HMM sequence search