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 3 is now available!

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


MetaPhlAn 3.0 useful links

Bug reports should be submitted via the repository issues tracking system.
For user support, consult the user manual or ask a question in our user support group, or contact directly the Segata lab.

MetaPhlAn 3.0 citation

At this moment, a manuscript for MetaPhlAn 3 is not available.
If used MetaPhlAn 3.0 for your research, please consider citing the MetaPhlAn2 paper:

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



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