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Flapjack Help

For more information on Flapjack, or to download the application, please visit the Flapjack web site.

.. toctree::
   :maxdepth: 2
   :caption: Getting started

   quickstart

.. toctree::
   :maxdepth: 2
   :caption: Dealing with data

   projects_&_data_formats
   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
   analysis_results_tables

.. toctree::
   :maxdepth: 2
   :caption: Miscellaneous topics

   preferences
   tips_&_shortcuts
   command_line_support


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