StrainPhlAn - A metagenomic strain-level population genomics tool

StrainPhlAn is a computational tool for performing metagenomic strain-level population genomics on large metagenomic datasets by profiling microbes from known species with strain level resolution and providing comparative and phylogenetic analyses of strains retrieved from metagenomic samples.

StrainPhlAn takes as input a set of metagenomic samples (in fastq format), reference genomes (in fasta) and then reconstructs the sample-specific strains of all species present in the samples and the genome-specific strains from reference genomes. The figure below shows the StrainPhlAn framework and its application for Prevotella copri on a subset of the samples considered from nine studies.


Software repository and supporting material

Software repository of StrainPhlAn:

The StrainPhlAn manual:

The StrainPhlAn tutorial:

User support (email-based group and discussion forum):

For comments and question please write to our
user support group:
or contact directly the Segata lab.


If you find this tool useful in your research, please cite our papers:

Francesco Beghini1 Lauren J McIver2 Aitor Blanco-Mìguez1 Leonard Dubois1 Francesco Asnicar1 Sagun Maharjan2,3 Ana Mailyan2,3 Andrew Maltez Thomas1 Paolo Manghi1 Matthias Scholz2,3 Mireia Valles-Colomer1 George Weingart2,3 Yancong Zhang2,3 Moreno Zolfo1 Curtis Huttenhower2,3 Eric A Franzosa2,3 Nicola Segata1,5

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3


1 Department CIBIO, University of Trento, Italy

2 Harvard T. H. Chan School of Public Health, Boston, MA, USA

3 The Broad Institute of MIT and Harvard, Cambridge, MA, USA

4 Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, Italy

5 IEO, European Institute of Oncology IRCCS, Milan, Italy

Duy Tin Truong1 Adrian Tett1 Edoardo Pasolli1 Curtis Huttenhower2 Nicola Segata1

Microbial strain-level population structure and genetic diversity from metagenomes

Genome Research(2017) 10.1101/gr.216242.116

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

2 Harvard T.H. Chan School of Public Health