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Integrated toolkit for analysis and evaluation of annotated genomes

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# AEGeAn Toolkit: analysis and evaluation of genome annotations

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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](https://brendelgroup.github.io/) philosophy: it generates **reproducible**, **accurate**, and **meaningful** results; it is **open** (source) and designed to be **scalable** and **easy** to use.

## Installation

Please find detailed installation instructions and options in the [INSTALL](./INSTALL.md) document.

## FAQ

Please see [our wiki FAQ pages](https://github.com/BrendelGroup/AEGeAn/wiki/FAQ) for usage examples and suggestions.

## Documentation

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.

## Contact

Please direct all comments and suggestions to [Volker Brendel](<mailto:vbrendel@indiana.edu>) or [Daniel Standage](<mailto:daniel.standage@nbacc.dhs.gov>).

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