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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 reflects 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" links 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?
• Gap Handling Explained
• [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)
• 3.0 Development Roadmap