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This wiki is currently being written and information in it may not yet be accurate.

Welcome to the Prodigal wiki. Here you will find plenty of information to get you started predicting genes in your favorite bug. This wiki has been written to reflect the options and behavior of the coming version, Prodigal 3.0.0. If you are using a 2.x release, you should look for the Prodigal 2.x tags in each page; these sections provide the correct information for the older version.

• What is Prodigal?
• Installing Prodigal
  • Installing on Mac OS X
  • Installing on Generic Unix
  • Installing on Windows
• Gene Prediction Modes
  • Normal Mode
  • Anonymous Mode
  • Training Mode
• Advice by Input Type
  • Finished Genomes
  • Draft Genomes
  • Metagenomes
  • Alternate Genetic Codes
  • Organisms with Gene Decay
  • Plasmids, Phages, Viruses, and Other Short Sequences
• Understanding the Prodigal Output
  • Gene Coordinates
  • Protein Translations
  • Nucleotide Sequences
  • Starts File
  • Summary Statistics
• Options Cheat Sheet
• [Next Steps](https://www.github.com/hyattpd/prodigal/wiki/Next Steps)
  • [Complete Annotation Options](https://www.github.com/hyattpd/prodigal/wiki/Next Steps#Complete Annotation Options)
  • [Visualization Options](https://www.github.com/hyattpd/prodigal/wiki/Parameters#Visualization Options)
• References