PhiSpy pipeline

PhiSpy specifications


Unique identifier OMICS_11703
Name PhiSpy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python, R
Computer skills Advanced
Version 2.3
Stability Stable
Maintained Yes


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  • person_outline Sajia Akhter <>

Publication for PhiSpy

PhiSpy citation

PMCID: 5721377

[…] five consecutive prophage genes), ‘−w=30’ (a window size of 30 orfs), and ‘−t  =  0’ (generic test set) settings. an rcgta-like region was classified as a putative prophage if it overlapped with a phispy-detected prophage region., presence of viral integrases was assessed within all prophage-like and rcgta-like regions, as well as among five orfs upstream and downstream of the regions. […]

PhiSpy institution(s)
Computational Science Research Center, San Diego State University, San Diego, CA, USA; Department of Computer Science, San Diego State University, San Diego, CA, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Egypt; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
PhiSpy funding source(s)
Advances in Bioinformatics from the National Science Foundation (DBI 0850356)

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