Graphical genotype visualization

Graphical genotype visualization

Flapjack provides a high performance visual interface into graphical genotyping applications in genetics and plant breeding, enabling rapid navigation and comparison between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.


Recently we've focussed on adding analysis functions to Flapjack. Most importantly we have added a Marker Assisted Backcrossing (MABC) analysis to Flapjack to support Genomic Selection projects, as well as a Pedigree Verification of Known Parents analysis. This is an active area of development and we plan to include more analyses in future releases of Flapjack..


We have recently published a paper on the Germinate 3 platform.

Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L., Thomas, W.T.B., Flavell, A.J. and Marshall, D. Flapjack – graphical genotype visualization. Bioinformatics 26(24), 3133-3134. doi: https://doi.org/10.1093/bioinformatics/btq580

Why Flapjack?

Flapjack has been designed to cope with modern high density genotype datasets.



You can grab the latest version of Flapjack from our download page. You can install Flapjack on Windows, Linux and macOS. You can download sample data from within Flapjack and get started straight away.



The Flapjack documentation covers all major features of Flapjack, including detailing the data formats required for loading data into Flapjack, as well as using the visualizations and analyses.

More Info

Source Code

Flapjack is an open source project, you can visit our subversion repository to get the source code.

More Info


The Flapjack development team.

Iain Milne

Iain has provided code that allows us to convert extracted data from Germinate in to Flapjack format.

Gordon Stephen

Gordon has recently become involved with Germinate and focuses on Germinate integration with BrAPI.

David Marshall

David provides scientific advice and promotes the project and its benefits on his travels.


Flapjack has been developed in close collaboration with the following funders.


If you have any questions about Flapjack, are having problems, want to let us know about bugs, or have ideas on how we can improve the Flapjack please contact us. flapjack@hutton.ac.uk

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