Flapjack Help
=============

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
   

.. _Flapjack web site: https://ics.hutton.ac.uk/flapjack