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MetaPhlAn: Metagenomic Phylogenetic Analysis

install with bioconda PyPI - Downloads MetaPhlAn on DockerHub Build MetaPhlAn package

What's new in version 3

  • New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
  • Estimation of metagenome composed by unknown microbes with parameter --unknown_estimation
  • Automatic retrieval and installation of the latest MetaPhlAn database with parameter --index latest
  • Virus profiling with --add_viruses
  • Calculation of metagenome size for improved estimation of reads mapped to a given clade
  • Inclusion of NCBI taxonomy ID in the ouput file
  • CAMI (Taxonomic) Profiling Output Format included
  • Removal of reads with low MAPQ values


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 the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:

  • unambiguous taxonomic assignments;
  • accurate estimation of organismal relative abundance;
  • species-level resolution for bacteria, archaea, eukaryotes and viruses;
  • strain identification and tracking
  • orders of magnitude speedups compared to existing methods.
  • metagenomic strain-level population genomics

If you use MetaPhlAn, please cite:

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata. eLife (2021)

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)


The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured you Anaconda installation in order to fetch packages from Bioconda, please follow these steps in order to setup the channels.

You can install MetaPhlAn by running

$ conda install -c bioconda python=3.7 metaphlan

For installing it from the source code and for further installation instructions, please see the Wiki at the Installation paragraph.

MetaPhlAn and StrainPhlAn tutorials and resources

In addition to the information on this page, you can refer to the following additional resources.