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StrainPhlAn specifications


Unique identifier OMICS_16926
Name StrainPhlAn
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of metagenomic samples and reference genomes.
Input format FASTA, FASTQ
Output data The sample-specific strains of all species present in the samples and the genome-specific strains from reference genomes.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Duy Tin Truong

Publication for StrainPhlAn

StrainPhlAn citations


Profiling microbial strains in urban environments using metagenomic sequencing data

Biol Direct
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] StrainPhlAn [] is a tool for identifying the specific strain of a given species within a metagenome. The tool is designed to track strains across large collections of samples and takes as input the ra […]


On the Road to Strain Resolved Comparative Metagenomics

PMCID: 5850074
PMID: 29556534
DOI: 10.1128/mSystems.00190-17

[…] MetaMLST () exploits a few species-specific hypervariable loci previously defined mostly for (opportunistic) pathogens and can rely on several thousands of already characterized strain profiles. With StrainPhlAn (), we brought to metagenomics the single-nucleotide variant (SNV) analysis that is routinely applied to the core genome of sequenced microbial isolates. This tool uses millions of referen […]


A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Genome Med
PMCID: 5704459
PMID: 29183332
DOI: 10.1186/s13073-017-0490-5

[…] composition was calculated with HUMANn2 [] using the UniRef90 database with default settings. Differentially abundant species were identified using MaAsLin. Strain-level analysis was performed using StrainPhlAn [] with the default parameters and PanPhlAn [] with (--min_coverage 1 --left_max 1.70 --right_min 0.30). While strain-level profiling using StrainPhlAn was carried out for 72 species of th […]


Unexplored diversity and strain level structure of the skin microbiome associated with psoriasis

PMCID: 5481418
PMID: 28649415
DOI: 10.1038/s41522-017-0022-5

[…] ere built by applying RAxML (with parameters “–m GTRCAT –p 1234”) on the sample-specific variants of species-specific marker genes extracted from the samples and the reference genomes performed using StrainPhlAn. For each metagenome, the reads were first mapped against the MetaPhlAn 2 markers by Bowtie2 and the mapping post-processed to produce the consensus sequence for the mapped reads. These co […]


Studying Vertical Microbiome Transmission from Mothers to Infants by Strain Level Metagenomic Profiling

PMCID: 5264247
PMID: 28144631
DOI: 10.1128/mSystems.00164-16

[…] consensus sequences are multiply aligned using MUSCLE version v3.8.1551 () (default parameters), and the phylogeny is reconstructed using RAxML version 8.1.15 () (parameters: -m GTRCAT and -p 1234). StrainPhlAn is available with supporting documentation at […]

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StrainPhlAn institution(s)
Centre for Integrative Biology, University of Trento, Trento, Italy; Biostatistics Department, Harvard School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA
StrainPhlAn funding source(s)
This work was supported in part by NIH grants R01HG005969 and U54DE023798, NSF grant DBI-1053486 and Army Research Office grant W911NF-11-1-0473, Fondazione Caritro grant Rif. Int.2014.0325, European Union H2020 Marie-curie grant (707345), a European Union FP7 Marie-Curie grant (PCIG13-618833), MIUR grant FIR RBFR13EWWI, Fondazione Caritro grant Rif. Int.2013.0239, Leo Pharma Research Foundation, and Terme di Comano grants.

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