Information & Computational Sciences

Download Flapjack

The most recent release of Flapjack is (7th October 2020). View the release notes to see what’s new.

Windows and macOS installers are digitally signed by The James Hutton Institute (checksums can be viewed here).

Please use the links below to download the Flapjack installer most suitable for your operating system. Flapjack is currently available for:

icon_windows Windows (64 bit)

icon_linux Linux (64 bit)

icon_osx macOS

Alternatively, if you use Bioconda, then Flapjack can be installed with: conda install flapjack

Our installers are built using the multi-platform installer builder install4j.

Follow the instructions provided by the graphical installer to install Flapjack. Note that Flapjack should not require administrator privileges to install or run (except for .rpm/.deb versions), but if you have any problems, don’t hesitate to contact us at

Flapjack is primarily developed on Windows 10, and gets additional regular testing on macOS and Centos.

Archived versions

You can download a limited selection of older copies of Flapjack from our archive. If you do need to return to an older version (for whatever reason), please let us know why.

Source code

For access to source code, please visit Flapjack’s GitHub repository.

Open source sponsors

The following companies have very kindly provided open source licences for their products to assist in the development of Flapjack.