The AEGeAn Toolkit provides a bundle of software tools for evaluating gene structure annotations and genome organization. The LocusPocus program is designed a break down an annotated eukaryotic genome into its constituent parts, and the fidibus workflow brings in a variety of other programs and scripts to summarize genome content and the spacing genes. The code conforms to our RAMOSE philosophy: it generates reproducible, accurate, and meaningful results; it is open (source) and designed to be scalable and easy to use.

Please find detailed installation instructions and options in the INSTALL document.

Please see our wiki FAQ pages for usage examples and suggestions.

The main AEGeAn Toolkit documentation is available at https://aegean.readthedocs.io/en/stable/. This documentation is focused on the core C library and the programs that directly call this library.

Documentation for the fidibus module, recently merged into AEGeAn, is available from the original (and now deprecated) GenHub project.

• quick start: https://github.com/standage/genhub/#quick-start-example-usages
• user manual: https://github.com/standage/genhub/blob/master/docs/MANUAL.md
• developer documentation: https://github.com/standage/genhub/blob/master/docs/DEVELOP.md

We are in the process of combining and standardizing these separate sources of documentation.

Please direct all comments and suggestions to Volker Brendel or Daniel Standage.