MetaPhlAn2 - An enhanced metagenomic taxonomic profiling tool

MetaPhlAn2 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. MetaPhlAn2 is also able 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.

MetaPhlAn2 relies on ~1M unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 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.

Software repository and supporting material

Software repository of MetaPhlAn2:

The MetaPhlAn2 tutorial:

The marker information file.

The marker sequences of the MetaPhlAn2 database in fasta format.
How to obtain.

The HMP profiles.

User support (email-based group and discussion forum):!forum/metaphlan-users

For comments and question please write to our
user support group:
or contact directly the Segata lab.


If you find this tool useful in your research, please cite our paper:

Duy Tin Truong, Eric Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Nature Methods 12, 902–903 (2015)

Some examples

Example of MetaPhlAn2 profiling on HMP and HMPII samples (microbial species and samples are hierarchically clustered).

MetaPhlAn2 profiling on HMP and HMPII

Example of strain level fingerprinting for Prevotella copri in HMP/HMPII gut samples at multiple time points. Prevotella copri strains of the same subjects are clustered together. The clustering step was performed based on Hamming distance.

Prevotella Copri strain level fingerprinting