PhiSpy Documentation ==================== .. image:: https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4 :target: https://edwards.flinders.edu.au/ :alt: Edwards Lab .. image:: https://www.zenodo.org/badge/60999054.svg :target: https://www.zenodo.org/badge/latestdoi/60999054 :alt: DOI .. image:: https://img.shields.io/badge/License-MIT-yellow.svg :target: https://opensource.org/licenses/MIT :alt: License: MIT .. image:: https://img.shields.io/pypi/pyversions/phispy.svg?style=flat-square&label=PyPi%20Versions :target: https://pypi.org/project/PhiSpy/ :alt: PyPI .. image:: https://img.shields.io/conda/dn/bioconda/phispy.svg?style=flat-square&label=BioConda%20install :target: https://anaconda.org/bioconda/phispy :alt: BioConda Install What is PhiSpy? --------------- PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome, it will use several approaches to identify the most likely prophage regions. PhiSpy was originally written by: * Sajia Akhter (sajia@stanford.edu) * Edwards Bioinformatics Lab (http://edwards.sdsu.edu/research/) Improvements, bug fixes, and other changes were made by: * Katelyn McNair - Edwards Bioinformatics Lab * Przemysław Decewicz - DEMB at the University of Warsaw Citation -------- If you use PhiSpy in your work, please cite: Sajia Akhter, Ramy K. Aziz, Robert A. Edwards; PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. *Nucleic Acids Research* 2012; 40 (16): e126. doi: `10.1093/nar/gks406 `_ For the newest versions, please also cite: McNair, K., Decewicz, P., Akhter, S., Aziz, R.K., Daniel, S., Edwards, R.A. 2019. PhiSpy. https://github.com/linsalrob/PhiSpy/ doi://10.5281/zenodo.3475717 Contents -------- .. toctree:: :maxdepth: 2 :caption: User Guide installation quickstart usage output training tips .. toctree:: :maxdepth: 2 :caption: Reference parameters exit_codes Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`