Alignment Window Annotations Menu Since Jalview 2.8.2

• Show Annotations
  If this is selected the "Annotation Panel" will be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
• Show Alignment Related
  Show all annotations that are for the alignment as a whole (for example, Consensus, or secondary structure prediction from alignment)).
• Hide Alignment Related
  Hide all annotations that are for the alignment as a whole.
• Show Sequence Related
  Show all annotations that are for individual sequences.
• Hide Sequence Related
  Hide all annotations that are for individual sequences.
• Show Alignment Related
  Show all annotations that are for the alignment as a whole (for example, Consensus).
• You can also selectively show or hide annotations from the Popup or Annotation menus.
• Sort by Sequence
  Sort sequence-specific annotations by sequence order in the alignment (and within that, by label).
• Sort by Label
  Sort sequence-specific annotations by label (and within that, by sequence order). If neither sort order is selected, no sorting is applied, allowing you to make a manual ordering of the annotations.
• Show Secondary Structure (since 2.11.4.0)
  All and None control display of secondary structure annotations on the alignment. Additional options allow just a specific source of Protein secondary structure to be shown.
• Autocalculated Annotation
  Settings for the display of autocalculated annotation.
  • Show first
    Show autocalculated annotations above sequence-specific annotations. Note this also applies to other annotations for the alignment, for example secondary structure prediction from alignment.
  • Show last
    Show autocalculated / alignment annotations below sequence-specific annotations.
  • Apply to all groups
    When ticked, any modification to the current settings will be applied to all autocalculated annotation.
  • Show Consensus Histogram
    Enable or disable the display of the histogram above the consensus sequence.
  • Show Consensus Logo
    Enable or disable the display of the Consensus Logo above the consensus sequence.
  • Show SS Consensus Histogram
    Enable or disable the display of histogram for Secondary Structure Consensus.
    
    Note: consensus secondary structure rows are not shown when no secondary structure annotations are present for sequences in the alignment. Use Add Reference Annotation from the sequence or selection popup menu to add annotations from structures or secondary structure predictions associated with the sequences in the alignment.
  • Normalise Consensus Logo
    When enabled, scales all logo stacks to the same height, making it easier to compare symbol diversity in highly variable regions.
  • Group Conservation
    When ticked, display a conservation row for all groups (only available for protein alignments).
  • Group Consensus
    When ticked, display a consensus row for all groups.
  • Group Secondary Structure Consensus
    When ticked, display a consensus secondary structure row for all groups.