Useful links

Software repository
User forum
Documentation

MetaPhlAn

MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data.
StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics. For details on StrainPhlAn, visit its dedicated website.


 

MetaPhlAn 4 relies on unique clade-specific marker genes identified from >1M microbial genomes (including reference genomes and metagenome assembled genomes) spanning dozens of thousands species-level genome bins (SGBs). MetaPhlAn 4 allows unambiguous taxonomic assignment and accurate SGB-level organismal relative abundance estimation for bacteria, archaea, and eukaryotes. Since MetaPhlAn 4.1, a newly developed viral module relying on a custom viral sequence database allows the metagenomic profiling of viruses alongside the traditional MetaPhlAn taxonomic profiling.

Installation

MetaPhlAn 4.1 is available in Bioconda and can be installed with Conda by running:
conda install -c bioconda metaphlan

Further installation instructions can be found in the documentation.


 

MetaPhlAn 4 useful links

MetaPhlAn 4 citations

If you use MetaPhlAn 4, please cite:

Aitor Blanco-Miguez1 Francesco Beghini1 Fabio Cumbo1 Lauren J McIver2,3 Kelsey N Thompson2,3 Moreno Zolfo1 Paolo Manghi1 Leonard Dubois1 Kun D Huang1 Andrew Maltez Thomas1 Gianmarco Piccinno1 Elisa Piperni1,4 Michal Punčochář1 Mireia Valles-Colomer1 Adrian Tett1,5 Francesca Giordano6 Richard Davies6 Jonathan Wolf6 Sarah E. Berry7 Tim D Spector8 Eric A Franzosa2,3 Edoardo Pasolli9 Francesco Asnicar1 Curtis Huttenhower2,3 Nicola Segata1,4

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology(2023) https://doi.org/10.1038/s41587-023-01688-w

1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy

5 Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria

6 Zoe Global, London, UK

7 Department of Nutritional Sciences, King’s College London, London, UK

8 Department of Twin Research, King’s College London, London, UK

9 Department of Agricultural Sciences, University of Naples, Naples, Italy

If you use the MetaPhlAn 4 viral module, please cite the MetaPhlan 4 paper and the viral module paper:

Moreno Zolfo1,2 Andrea Silverj1,3,4 Aitor Blanco-Miguez1 Paolo Manghi1 Omar Rota-Stabelli1,3,4 Vitor Heidrich1 Jordan Jensen5 Sagun Maharjan5 Eric Franzosa5 Cristina Menni6 Alessia Visconti7 Federica Pinto1 Matteo Ciciani1 Curtis Huttenhower5 Anna Cereseto1 Francesco Asnicar1 Hiroaki Kitano2,8,9 Takuji Yamada2,10,11,12,13 Nicola Segata1,14

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples

bioRxiv(2024) https://doi.org/10.1101/2024.02.19.580813

1 Department CIBIO, University of Trento, Italy

2 Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan

3 Center Agriculture Food Environment (C3A), University of Trento, Italy

4 Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy

5 Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA

6 Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK

7 Center of Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy

8 The Systems Biology Institute (SBI), Tokyo, Japan

9 IOM Bioworks Pvt. Ltd., Centre for Cellular and Molecular Platforms (C-CAMP), GKVK Post, Bellary Rd, Bengaluru, Karnataka-560065, India

10 School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan

11 Metagen, Inc., Yamagata, Japan

12 Metagen Therapeutics, Inc., Yamagata, Japan

13 Digzyme, Inc., Tokyo, Japan

14 Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy


 

MetaPhlAn 3

MetaPhlAn 3 is available in Bioconda and can be installed with Conda by running:
conda install -c bioconda metaphlan=3.1.0

Francesco Beghini1 Lauren J McIver2 Aitor Blanco-Miguez1 Leonard Dubois1 Francesco Asnicar1 Sagun Maharjan2,3 Ana Mailyan2,3 Andrew Maltez Thomas1 Paolo Manghi1 Matthias Scholz2,3 Mireia Valles-Colomer1 George Weingart2,3 Yancong Zhang2,3 Moreno Zolfo1 Curtis Huttenhower2,3 Eric A Franzosa2,3 Nicola Segata1,5

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife(2021) https://doi.org/10.7554/eLife.65088

1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, Italy

5 IEO, European Institute of Oncology IRCCS, Milan, Italy


 

MetaPhlAn2

If you are interested in using the previous version, MetaPhlAn2, the source code is available on GitHub.
We advise to install it using Conda by running:
conda install -c bioconda metaphlan2=2.8

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Duy Tin Truong Eric Franzosa Timothy L Tickle Matthias Scholz George Weingart Edoardo Pasolli Adrian Tett Curtis Huttenhower Nicola Segata

Nature Methods(2015) https://doi.org/10.1038/nmeth.3589