Parsnp statistics

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Associated diseases

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Parsnp specifications


Unique identifier OMICS_21461
Name Parsnp
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data a directory of files to be aligned
Input format MultiFASTA
Output data A single binary file encoding the reference genome, annotations, alignment, variants, and tree.
Output format BED, GenBank, FASTA, MAF, Newick, VCF, XMFA.
Operating system Unix/Linux, Mac OS
Programming languages C++, Python, Shell (Bash)
Parallelization OpenMP
Computer skills Advanced
Version 1.2
Stability Stable
gcc compiler, OpenMP
Maintained Yes



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  • person_outline Todd J. Treangen <>

Additional information

Publication for Parsnp

Parsnp in publications

PMCID: 5942804
PMID: 29742151
DOI: 10.1371/journal.pone.0197053

[…] differences in the proportions of virulence markers between lineages were considered significant when p < 0.05., single nucleotide polymorphisms (snps) were identified among all genomes using parsnp with parameters set to default with a recombination filter (-x), all genomes included (-c), and random reference genome selection (-r!) which chose genome ars-cc9338 []. a maximum likelihood […]

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] e. coli 1094 sequence was aligned against selected genomes belonging to e. coliphylogenetic group a. alignment and posterior nj (neighbor joining) phylogenetic reconstruction was carried out with parsnp, a fast core-genome multi-aligner, using default parameters []. alignment and tree visualization was done with gingr, a dynamic visual platform (fig. ) []., we selected five e. coli genomes […]

PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] from trimmed reads. see file s1 for specific commands and settings used for each program., an alignment of orthologous sequences conserved in all genomes was generated from de novo assemblies using parsnp, with the –c option invoked to force inclusion of all genomes. reference genomes e. fergusonii (nc_011740.1) and e. coli tw10509 (nz_gl872204.1) were included to provide phylogenetic context […]

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17

[…] sequence (accession no. nc_013321.1) ()., a whole-genome alignment of de novo-assembled contigs from 539 cc8 strains from this study and 24 cc8 strains described in other papers was processed using parsnp (). the alignment length was 2,361,133 bp. potential recombination sites were identified using clonalframeml () based on a maximum likelihood (ml) guide tree constructed by phyml (, ), removed […]

PMCID: 5938774
PMID: 29664388
DOI: 10.3201/eid2405.171700

[…] based on 7 housekeeping genes (, single-nucleotide polymorphisms (snps) were called using harvest version 1.0.1 ( (). we used parsnp, a component of the harvest suite, to align the assembled genomes and define the core genome. we identified snps for both chromosomes by parsnp in the multi-alignments; we used filtered […]

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Parsnp institution(s)
National Biodefense Analysis and Countermeasures Center, MD, USA
Parsnp funding source(s)
Supported by an Agreement (No. HSHQDC-07-C-00020) awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC); and a Federally Funded Research and Development Center.

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