PanPhlAn /

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PanPhlAn - strain detection and characterization

Pangenome-based Phylogenomic Analysis

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.

PanPhlAn is written in Python and covers the three main tasks:

  •, to create the pangenome database of a bacterial species
    → read more
  •, to profile each metagenomic sample by mapping it against the species specific database
    → read more
  •, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices
    → read more

PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:

  • Bowtie2
  • Samtools
  • Usearch 7 (only for generating your own species database)
  • Python version 2.7 or 3.x (including the Biopython module)

For more information, see our wiki → Download and Installation.

Contact & User support

→ User Tutorial
→ User forum

The PanPhlAn software team: Matthias Scholz (algorithm design), Thomas Tolio (programmer), and Nicola Segata (principal investigator).
For help, write to

PanPhlAn is a project of the Computational Metagenomics Lab at CIBIO, University of Trento, Italy