Alignment Window Annotations Menu Since Jalview 2.8.2

- 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.
- 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.
  - 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.