This release is a pre-release and may not be stable for production use.
MetaPhlAn: Metagenomic Phylogenetic Analysis
What's new in version 4
- Adoption of the species-level genome bins system (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html)
- New MetaPhlAn marker genes extracted identified from ~1M microbial genomes
- Ability to profile 21,978 known (kSGBs) and 4,992 unknown (uSGBs) microbial species
- Better representation of, not only the human gut microbiome but also many other animal and ecological environments
- Estimation of metagenome composed by microbes not included in the database with parameter
--unclassified_estimation - Compatibility with MetaPhlAn 3 databases with parameter
--mpa3
Description
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling. MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them taxonomically unidentified at the species level, allowing:
- unambiguous taxonomic assignments;
- an accurate estimation of organismal relative abundance;
- SGB-level resolution for bacteria, archaea and eukaryotes;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
- metagenomic strain-level population genomics
If you use MetaPhlAn, please cite:
Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4. Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Preprint (2022)
If you use StrainPhlAn, please cite the MetaPhlAn paper and the following StrainPhlAn paper:
Microbial strain-level population structure and genetic diversity from metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017)
MetaPhlAn and StrainPhlAn tutorials and resources
In addition to the information on this page, you can refer to the following additional resources.
-
Related tools including PanPhlAn (and its tutorial), GraPhlAn (and it tutorial), PhyloPhlAn 3 (and its tutorial), HUMAnN (and its tutorial).
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The related bioBakery workflows
Release files for metaphlan 4b3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| MetaPhlAn-4b3.tar.gz | 1.1 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| MetaPhlAn-4b3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 2.3 MB
Release files / MetaPhlAn-4b3.tar.gz
| Download URL | MetaPhlAn-4b3.tar.gz |
|---|---|
| Size | 1.1 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.7.13
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Release files / MetaPhlAn-4b3-py3-none-any.whl
| Download URL | MetaPhlAn-4b3-py3-none-any.whl |
|---|---|
| Size | 1.2 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
330b82dad997f037bf11c1ea549b617057ca9ae035e3289550fe4395bce56094
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.7.13
|
