panphlan 1.3

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.

The newest version PanphlAn 3.0 is available here

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:

• panphlan_pangenome_generation.py, to create the pangenome database of a bacterial species
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• panphlan_map.py, to profile each metagenomic sample by mapping it against the species specific database
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• panphlan_profile.py, to merge and process the mapping results for getting the final gene presence/absence and transcriptional matrices
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PanPhlAn runs under Ubuntu/Linux and requires the following software tools to be installed on your system:

• Bowtie2
• Samtools
• Python 3.x (including the Biopython module)

For more information, see our wiki Download and Installation.

Contact & User support

A user tutorial is available on the PanPhlAn wiki. For help, use also the bioBakery help forum.

The PanPhlAn software team: Matthias Scholz (algorithm design), Thomas Tolio (programmer), Leonard Dubois and Nicola Segata (principal investigator).

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