Model type
Marker-based taxonomic profiler; this record is the paper-specific evaluated configuration.
Configuration
MetaPhlAn3
MetaPhlAn3 is the marker-based metagenomic comparator in the NABAS+ study.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 4); Introduction (paragraph 4)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6)At a glance
Biological inputs
Shotgun metagenomic reads and a versioned marker database
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Discussion (paragraph 6); Introduction (paragraph 3)Outputs
Taxonomic abundance profiles
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 8); Materials and methods/Datasets and reference databases/Recreating the CAMI sample19 (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| MetaPhlAn3: Metagenomic taxonomic classification Configuration: MetaPhlAn3Task: Metagenomic taxonomic classificationDataset: CAMI II Toy human gastrooral sample19-new Newly generated sample19 used for classifier comparison. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.753 F1 score Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Table 3, Sample19-new / MetaPhlAn3 row, F1 score column Source checking is not independent reproduction. |
How it works
How the evaluated method works
Taxonomic profiling uses clade-specific marker information to estimate microbial composition from shotgun reads.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6)Underlying method and version boundaries
MetaPhlAn profiles taxonomic composition using a marker reference. The repository’s current release is not the historical MetaPhlAn3 configuration; software and database versions require separate identification.
Sources
biobakery/MetaPhlAn README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies MetaPhlAn3: Metagenomic taxonomic classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-040Strengths and limitations
Strengths and considerations
- Provides a marker-based reference against whole-genome alignment and k-mer classification.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking (paragraph 1); Discussion (paragraph 3)
Limitations and conditions
- The current MetaPhlAn release is not the version in this row; database and parameter choices are required for reproduction.
Sources
Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/Zymo community standards (paragraph 3); Materials and methods/Statistical comparison and visualization (paragraph 10)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-df4084611520b7Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · 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 | Marker-based taxonomic profiler; this record is the paper-specific evaluated configuration.Sourcesbiobakery/MetaPhlAn README.md · README.md model description |
| Architecture / procedure | Taxonomic profiling uses clade-specific marker information to estimate microbial composition from shotgun reads.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) |
| Biological inputs | Shotgun metagenomic reads and a versioned marker databaseSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Discussion (paragraph 6); Introduction (paragraph 3) |
| Outputs | Taxonomic abundance profilesSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 8); Materials and methods/Datasets and reference databases/Recreating the CAMI sample19 (paragraph 1) |
| Parameters | Not applicable: taxonomic marker profiling does not have a pretrained neural parameter total. · Not applicableSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking (paragraph 2); Materials and methods/Running the classifiers (paragraph 2) |
| Known versions / configuration | MetaPhlAn3, as named in the paper; no exact package/database hash is supplied by the catalogue row. · Not reported in inspected sourcesSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Reference-marker classification without task-specific neural fitting. CAMI comparisons use mpa_v31_CHOCOPhlAn_201901; a newer Zymo comparison uses mpa_vOct22_CHOCOPhlAnSGB_202212. These database conditions are not pooled.SourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods / Datasets and reference databases / CAMI samples and Zymo community standards, database lists |
| Context limits | Not applicable to a pretrained sequence-token window; read/contig lengths and the reference-database or comparison configuration determine the analysed input. · Not applicableSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Discussion (paragraph 6) |
| Access | Official upstream implementation and usage documentation: https://github.com/biobakery/MetaPhlAn/blob/424f3e6e30618266404353e1083c6405a9f02f48/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesbiobakery/MetaPhlAn README.md · README.md; installation, model download and usage instructions |
| Code licence | Repository-specific licence text is available; a standard SPDX label has not been established. (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesbiobakery/MetaPhlAn license.txt · license.txt; complete licence text |
| Weights licence | Not applicable to neural weights; the software and reference database have separate reuse terms. · Not applicableSourcesAdvancing metagenomic classification with NABAS+: a novel alignment-based approach · Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Datasets and reference databases/CAMI samples (paragraph 2) |
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 input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Shotgun metagenomic reads and a versioned marker database","MetaPhlAn3","Taxonomic abundance profiles"] Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Marker-based taxonomic profiler; this record is the paper-specific evaluated configuration. Individual claims | biobakery/MetaPhlAn README.md README.md model description Version: 424f3e6e30618266404353e1083c6405a9f02f48 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Taxonomic profiling uses clade-specific marker information to estimate microbial composition from shotgun reads. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence Not applicable to neural weights; the software and reference database have separate reuse terms. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Datasets and reference databases/CAMI samples (paragraph 3); Materials and methods/Datasets and reference databases/CAMI samples (paragraph 2) Version: PMC12231603.1 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Shotgun metagenomic reads and a versioned marker database Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Discussion (paragraph 6); Introduction (paragraph 3) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Taxonomic abundance profiles Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 8); Materials and methods/Datasets and reference databases/Recreating the CAMI sample19 (paragraph 1) Version: PMC12231603.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters Not applicable: taxonomic marker profiling does not have a pretrained neural parameter total. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Materials and methods/Selecting and setting up reference classifiers for NABAS+ benchmarking (paragraph 2); Materials and methods/Running the classifiers (paragraph 2) Version: PMC12231603.1 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration MetaPhlAn3, as named in the paper; no exact package/database hash is supplied by the catalogue row. Individual claims | Advancing metagenomic classification with NABAS+: a novel alignment-based approach Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: PMC12231603.1 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach · Original source · PMC12231603.1
- biobakery/MetaPhlAn README.md · Original source · 424f3e6e30618266404353e1083c6405a9f02f48
- biobakery/MetaPhlAn license.txt · Original source · 424f3e6e30618266404353e1083c6405a9f02f48
Technical metadata and extraction receipts
Stable ID: reported-model-df4084611520b7
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- MetaPhlAn3
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- 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: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: nabas-plus-2025; evidence-reported-base-metaphlan-readme-md; source locator: Materials and methods/Datasets and reference databases/Consent for sample collection (paragraph 1); Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 6) | README.md model description | Results/Creating a novel alignment-based metagenomic tool to improve classification accuracy and reduce false positives (paragraph 4); Introduction (paragraph 4); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.