For more information on Flapjack, or to download the application, please visit the Flapjack web site.
Tip
We now have a range of :doc:`videos` that you can watch to learn how to use Flapjack.
.. toctree:: :maxdepth: 2 :caption: Getting started quickstart
.. toctree:: :maxdepth: 2 :caption: Dealing with data projects_&_data_formats gobii_qtl pedigrees favalleles import_data duplicate_markers export_data quick_export_data export_image
.. toctree:: :maxdepth: 2 :caption: Visualizing genotypes genotype_visualization modes_&_views selecting_lines_&_markers show_hide_lines show_hide_markers filtering_markers chromosome_map_scaling colour_schemes customize_colours allele_frequency_threshold bookmarks toggle_visible_displays create_new_view database_link_settings
.. toctree:: :maxdepth: 2 :caption: Other visualizations chromosome_visualization phenotype_visualization select_traits qtl_visualization filter_qtls graph_visualization
.. toctree:: :maxdepth: 2 :caption: Analysis features find_by_name sort_lines simmatrix_creation dendrogram_creation mabc mabc_tutorial pedver_f1s_known_parents pedver_f1s_known_parents_tut pedver_lines pedver_lines_tut forward_breeding ifb analysis_results_tables batch_analysis videos
.. toctree:: :maxdepth: 2 :caption: Miscellaneous topics preferences tips_&_shortcuts command_line_support allocating_memory