Method

MetaPhlAn

MetaPhlAn profiles microbial community composition from shotgun metagenomic reads using clade-specific marker genes.

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

0 evaluations · 0 metric rows

How it worksMetaPhlAn workflow

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

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

At a glance

Model type

Marker-based taxonomic profiling

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

Inputs

Shotgun metagenomic reads and a selected MetaPhlAn marker database.

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

Outputs

Taxonomic relative-abundance profiles; StrainPhlAn is a separate strain-level analysis.

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

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

MetaPhlAn profiles microbial community composition from shotgun metagenomic reads using clade-specific marker genes. Reference marker-gene profiling; MetaPhlAn 4 organizes reference and metagenome-assembled genomes into species-level genome bins. The documented inputs are shotgun metagenomic reads and a selected MetaPhlAn marker database. The output consists of taxonomic relative-abundance profiles; StrainPhlAn is a separate strain-level analysis.

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

Versions and reproducibility

MetaPhlAn 4 paper and 4.2-linked current documentation; database version is a separate reproducibility requirement. Shotgun reads; no fixed neural token context.

Sources (2)

biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

Strengths and limitations

Strengths supported by sources

Marker-based profiling can incorporate characterized and previously uncharacterized species groups.
Sources (2)
biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

Limitations and conditions

Coverage depends on the marker database and habitat. The MetaPhlAn 4 paper identifies remaining gaps for under-studied environmental communities; newer software/databases may have different scope.
Sources (2)
biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion

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: catalog-model-metaphlan

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	Marker-based taxonomic profiling Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Architecture	Reference marker-gene profiling; MetaPhlAn 4 organizes reference and metagenome-assembled genomes into species-level genome bins. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Inputs	Shotgun metagenomic reads and a selected MetaPhlAn marker database. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Outputs	Taxonomic relative-abundance profiles; StrainPhlAn is a separate strain-level analysis. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Parameters	Inapplicable as a neural parameter count. · Not applicable Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Known versions	MetaPhlAn 4 paper and 4.2-linked current documentation; database version is a separate reproducibility requirement. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Training data	Reference-derived marker database rather than neural pretraining; record the exact database release. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Context limits	Shotgun reads; no fixed neural token context. Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Weights licence	Inapplicable to this procedural method; marker databases have their own provenance and terms. · Not applicable Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Access	Official project documentation and implementation: https://github.com/biobakery/MetaPhlAn Sources (2) biobakery/MetaPhlAn: README.md; metaphlan: Journal full-text XML · README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion
Code licence	MIT Sources biobakery/MetaPhlAn: license.txt · license.txt: licence text
Assumptions	Not extracted or verified for this record.

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.

39 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	metaphlan: Journal full-text XML Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009254+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: `547306680d52f70865906db567dee93323ecdec3b2e162608dff5057e057aa4b` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	biobakery/MetaPhlAn: README.md Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 424f3e6e30618266404353e1083c6405a9f02f48 Retrieved: 2026-09-16T19:46:18.561509+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: `ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Metagenomic reads","Marker-gene mapping","Species-group quantification","Relative-abundance profile"] Individual claims	metaphlan: Journal full-text XML Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009254+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: `547306680d52f70865906db567dee93323ecdec3b2e162608dff5057e057aa4b` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Metagenomic reads","Marker-gene mapping","Species-group quantification","Relative-abundance profile"] Individual claims	biobakery/MetaPhlAn: README.md Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 424f3e6e30618266404353e1083c6405a9f02f48 Retrieved: 2026-09-16T19:46:18.561509+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: `ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title MetaPhlAn workflow Individual claims	metaphlan: Journal full-text XML Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009254+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: `547306680d52f70865906db567dee93323ecdec3b2e162608dff5057e057aa4b` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title MetaPhlAn workflow Individual claims	biobakery/MetaPhlAn: README.md Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 424f3e6e30618266404353e1083c6405a9f02f48 Retrieved: 2026-09-16T19:46:18.561509+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: `ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Marker-based taxonomic profiling Individual claims	metaphlan: Journal full-text XML Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009254+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: `547306680d52f70865906db567dee93323ecdec3b2e162608dff5057e057aa4b` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Marker-based taxonomic profiling Individual claims	biobakery/MetaPhlAn: README.md Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 424f3e6e30618266404353e1083c6405a9f02f48 Retrieved: 2026-09-16T19:46:18.561509+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: `ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Reference marker-gene profiling; MetaPhlAn 4 organizes reference and metagenome-assembled genomes into species-level genome bins. Individual claims	metaphlan: Journal full-text XML Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009254+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: `547306680d52f70865906db567dee93323ecdec3b2e162608dff5057e057aa4b` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Reference marker-gene profiling; MetaPhlAn 4 organizes reference and metagenome-assembled genomes into species-level genome bins. Individual claims	biobakery/MetaPhlAn: README.md Original source ↗ README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 424f3e6e30618266404353e1083c6405a9f02f48 Retrieved: 2026-09-16T19:46:18.561509+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: `ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7` 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

4 source records and release history

MetaPhlAn official resource · Original source · Not reported
biobakery/MetaPhlAn: README.md · Original source · 424f3e6e30618266404353e1083c6405a9f02f48
metaphlan: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
biobakery/MetaPhlAn: license.txt · Original source · 424f3e6e30618266404353e1083c6405a9f02f48

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Technical metadata and extraction receipts

Stable ID: catalog-model-metaphlan

areas: microbes-communities
method types: specialist
entity level: family
version: current marker database pinned at run time
reported name: MetaPhlAn
access: Public profiler; marker database version must be pinned separately.
method type: specialist
historical missing metadata: checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: not_yet_extracted
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-72fdaed158e4ff851fbe; evidence-official-37f825d1226e59cbbfbf; source locator: README.md: description; MetaPhlAn 4 paper: Building the expanded SGB catalog and Discussion; ambiguities: None recorded

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