About the PanPhlAn category

Name: PanPhlAn
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Description: 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.


Matthias Scholz1,* Doyle V. Ward2,* Edoardo Pasolli1,* Thomas Tolio1 Moreno Zolfo1 Francesco Asnicar1 Duy Tin Truong1 Adrian Tett1 Ardythe L. Morrow3 Nicola Segata1

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Nature Methods 13, 435–438, 2016.10.1038/nmeth.3802

  • Equal contribution

1 Centre for Integrative Biology, University of Trento, Trento, Italy

2 Center for Microbiome Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA

3 Department of Pediatrics, Perinatal Institute, Cincinnati, Ohio, USA