PhiSpy Documentation

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

User Guide

• Installation
  • Conda (Recommended)
  • PIP
  • Advanced Installation
  • Software Requirements
  • Optional Dependencies
  • Verifying Installation
• Quick Start
  • Testing PhiSpy
  • Basic Usage
  • Preparing Your Genome
  • Example Workflow
  • Common Use Cases
  • Next Steps
• Usage Guide
  • Basic Usage
  • Important Parameters
  • HMM Searches
  • Metrics
  • Advanced Usage
  • Interactive PhiSpy
  • Performance Optimization
  • Best Practices
  • Common Workflows
• Output Files
  • Choosing Output Files
  • Output File Descriptions
  • Assessing Predictions
  • Example Output
  • Best Practices
• Custom Training Sets
  • Why Create Training Sets?
  • Requirements
  • Marking Prophage Features
  • Creating Training Sets
  • Complete Example
  • Advanced Options
  • Best Practices
  • Troubleshooting
  • Example: Training for Novel Genus
  • Further Reading
• Tips and Tricks
  • PATH Issues
  • Installation Tips
  • Running PhiSpy
  • Parameter Tuning
  • Performance
  • Debugging
  • Common Issues
  • File Format Issues
  • Quality Control
  • Batch Analysis
  • Best Practices Summary
  • Getting Help
  • Useful Resources

Reference

• Command-Line Parameters
  • Basic Parameters
  • Algorithm Parameters
  • Metrics and Features
  • HMM Search Parameters
  • Annotation Parameters
  • Output Control
  • Evaluation and Debugging
  • Examples
• Exit Codes
  • Exit Code Reference
  • Detailed Descriptions
  • Handling Exit Codes in Scripts
  • Workflow Integration
  • Debugging Tips

Indices and tables

• Index

• Module Index

• Search Page