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 paper:

Duy Tin Truong1 Adrian Tett1 Edoardo Pasolli1 Curtis Huttenhower2 Nicola Segata1

Microbial strain-level population structure and genetic diversity from metagenomes

Genome Research in press (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