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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



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  • person_outline Duy Tin Truong <>

Publication for StrainPhlAn

StrainPhlAn in publications

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

[…] known sequence-types from 15 species of clinical relevance. for instance, we identified several acinetobacter strains that were close to the nosocomial opportunistic pathogen a. nosocomialis. with strainphlan, a generalized version of the metamlst approach, we inferred the phylogenetic structure of pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental […]

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

[…] () 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 […]

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 […]

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

[…] set of strain-level profiling methods we developed.– the first recently developed approach is an assembly free strain-level phylogenetic method based on species-specific metaphlan 2 markers, called strainphlan, which identifies strains looking at taxon-specific single-nucleotide polymorphisms (snps) (see methods) and allowed us to build two whole-genome phylogenetic trees of the two most common […]

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

[…] metagenomic samples at a finer strain-level resolution. this was achieved by applying a recent strain-specific pangenome-based method called panphlan (), as well as a genetics-based method called strainphlan (d. t. truong, a. tett, e. pasolli, c. huttenhower, and n. segata, submitted for publication) (see materials and methods), which identifies single-nucleotide variants (snvs) […]

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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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