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Welcome to the Prodigal wiki. Here you will find plenty of information to get you started predicting genes in your favorite bacteria. This wiki was created well after the release of Prodigal 2, and 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
• [Basic Gene Prediction](https://www.github.com/hyattpd/prodigal/wiki/Basic Gene Prediction)
  • [High Quality Genomes](https://www.github.com/hyattpd/prodigal/wiki/Basic Gene Prediction#HighQuality)
  • [Draft Genomes](https://www.github.com/hyattpd/prodigal/wiki/Basic Gene Prediction#Draft)
  • [Metagenomes](https://www.github.com/hyattpd/prodigal/wiki/Basic Gene Prediction#Metagenomes)
• Using Training Files
  • When Do I Need a Training File?
  • How Do I Use Training Files?
• Gene Finding Parameters
  • [Gaps and Partial Genes](https://www.github.com/hyattpd/prodigal/wiki/Parameters#Gaps and Partial Genes)
  • [RBS Motifs](https://www.github.com/hyattpd/prodigal/wiki/Parameters#RBS Motifs)
• [Understanding the Prodigal Output](https://www.github.com/hyattpd/prodigal/wiki/Prodigal Output)
  • [Gene Coordinates File](https://www.github.com/hyattpd/prodigal/wiki/Prodigal Output#Gene Coordinates)
  • [The Summary File](https://www.github.com/hyattpd/prodigal/wiki/Prodigal Output#Summary File)
  • [The Starts File](https://www.github.com/hyattpd/prodigal/wiki/Basic Gene Prediction#Starts File)
• [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
• 3.0 Development Roadmap