Parsnp specifications


Unique identifier OMICS_21461
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
Requirements gcc compiler, OpenMP
Maintained Yes



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  • person_outline Todd J. Treangen <>

Additional information

Parsnp article

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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