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  • ‘Flapjack’ – high-throughput genotype visualizer


    This multi-platform application allows the graphical observation of genotyping and haplotype visualization of SNP 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 allows analysis to run over the data, such as calculating similarity matrices, running Principal Coordinates Analysis (PCoA) calculations, or the generation of statistics to help with marker assisted backcrossing or pedigree verification of F1s. 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 graphical genotypes to identify associated haplotypes.
    4. Provides example data and information non-input file formats.
    5. Phenotypic data can be added to data to aid interpretation.
    6. It can contribute to the genetic diversity analysis.
    7. Explore data available in the MasAgro- Biodiversidad project.
    8. Multi-platform application available to the public to download.

     


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  • Comments

    For visualization of large genotypic data, this software is an excellent tool and interfaces with other software such as CurlyWhirly for visualization of PCoA analysis done by Flapjack.

     

    Availability

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

     

    Primary Users

    Breeders, researchers, students at public institutes and private seed companies who works with large set of genotypic data

     

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