MetaPhlAn
MetaPhlAn is a
computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution.
With StrainPhlAn, it is possible to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
MetaPhlAn 4 is now available!
MetaPhlAn 4 is available in Bioconda and can be installed with Conda by running:MetaPhlAn 4 useful links
- The MetaPhlAn 4 GitHub repository
- The user manual is available here
- For user support, please go to the BioBakery forum
- Synthetic metagenomes containing known and unknown SGBs are available here
- Single-isolate synthetic metagenomes at different coverages are available here
For user support, ask a question in our user support group, or contact directly the Segata lab.
MetaPhlAn 4 citation
bioRxiv(2022) https://doi.org/10.1101/2022.08.22.504593
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
MetaPhlAn 3
MetaPhlAn 3 is available in Bioconda and can be installed with Conda by running: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
We advise to install it using Conda by running: