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:

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

For user support, ask a question in our user support group, or contact directly the Segata lab.


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

Aitor Blanco-Miguez1 Francesco Beghini1 Fabio Cumbo1 Lauren J McIver2,3 Kelsey N Thompson2,3 Moreno Zolfo1 Paolo Manghi1 Leonard Dubois1 Kun D Huang1 Andrew Maltez Thomas1 Gianmarco Piccinno1 Elisa Piperni1,4 Michal Punčochář1 Mireia Valles-Colomer1 Adrian Tett1,5 Francesca Giordano6 Richard Davies6 Jonathan Wolf6 Sarah E. Berry7 Tim D Spector8 Eric A Franzosa2,3 Edoardo Pasolli9 Francesco Asnicar1 Curtis Huttenhower2,3 Nicola Segata1,4

Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4


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

5 Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria

6 Zoe Global, London, UK

7 Department of Nutritional Sciences, King’s College London, London, UK

8 Department of Twin Research, King’s College London, London, UK

9 Department of Agricultural Sciences, University of Naples, Naples, 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