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About the Metaphlan category

Name: MetaPhlAn
User manual || Tutorial

Description: 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.


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