MetaPhlAn v2.0

MetaPhlAn v2.0: Metagenomic Phylogenetic Analysis

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:

  • up to 25,000 reads-per-second (on one CPU) analysis speed (orders of magnitude faster compared to existing methods);
  • unambiguous taxonomic assignments as the MetaPhlAn markers are clade-specific;
  • accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction of reads);
  • species-level resolution for bacteria, archaea, eukaryotes and viruses;
  • extensive validation of the profiling accuracy on several synthetic datasets and on thousands of real metagenomes.

Obtaining MetaPhlAn v2.0

Download MetaPhlAn v2.0 ( ). Review the README or visit the MetaPhlAn v2.0 Bitbucket repository for information on installation and how to run.


MetaPhlAn v2.0 tutorial is also available here.

The tutorial contains a demo dataset and runs through basic command line instructions and the corresponding results.

Synthetic Metagenomes

Synthetic metagenomes can be accessed from here.

Technical Support

We provide support for MetaPhlAn v2.0 users.

Please join our MetaPhlAn v2.0 category in Forum designated specifically for MetaPhlAn v2.0 users. Feel free to post any questions on the forum directly.

Google Group metaphlan-users . (Getting deprecated soon)


Please cite MetaPhlAn v2.0 as below:
Metagenomic microbial community profiling using unique clade-specific marker genes

Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower.
Nature Methods, 8, 811–814, 2012