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  • ‘Flapjack’ – high-throughput genotype visualizer

    This multi-platform application allows graphing of genotypes and visualization of haplotypes for SNP (single nucleotide polymorphism) data, including those generated by high throughput and comparable genotyping technologies. Its visualizations are rendered in real-time, allowing for rapid navigation and comparisons between lines and markers. Flapjack also performs data analyses including calculating similarity matrices, Principal Coordinates Analysis (PCoA), and the calculating statistics to help with marker assisted backcrossing or F1 pedigree verification. Flapjack was developed by James Hutton Institute, in collaboration with CIMMYT.

    Product details and features

    1. Facilitates visualization of low to high-density genotypic data in mapped, unmapped or combined formats.
    2. Provides interactive visualizations of high-performance genotypic data (i.e. DArTseq), allowing fast navigation and genetic comparisons between lines, molecular markers and chromosomes.
    3. Any map-based information such as Quantitative Trait Locus (QTL) positions can be aligned against graphed genotypes to identify associated haplotypes.
    4. Provides example data and information in file formats ready to import and use.
    5. Phenotypic data can be added to genotypic data to facilitate interpretation.
    6. It is useful for genetic diversity analyses.
    7. It can explore data available in the MasAgro-Biodiversidad project.
    8. Multi-platform application publically available for download.

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    • Flapjack is an excellent tool for visualization of large genotypic data sets. It interfaces well with other software, such as CurlyWhirly, for visualization of PCoA analysis done by Flapjack.


    Released, with improved versions being periodically released with automatic upgrade https://ics.hutton.ac.uk/flapjack/download-flapjack/

    Primary Users

    Breeders, researchers and students who work with large sets of genotypic data

    For more information

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