Alignment Window View Menu

- New View (Control T)
  Creates a new view from the current alignment view.
- Expand Views (X)
  Display each view associated with the alignment in its own alignment window, allowing several views to be displayed simultaneously.
- Gather Views (G)
  Each view associated with the alignment will be displayed within its own tab on the current alignment window.
- Show→(all Columns / Sequences / Sequences and Columns )
  All hidden Columns / Sequences / Sequences and Columns will be revealed.
- Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
  Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
- 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.
- Autocalculated Annotation
  Settings for the display of autocalculated annotation.
  - 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 sequence 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).
  - Apply to all groups
    When ticked, display a consensus row for all groups.
- Automatic Scrolling
  When selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse pointer in a linked alignment or structure view.
- Show Sequence Features
  Show or hide sequence features on this alignment.
- Seqence Feature Settings...
  Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and retrieve features from DAS annotation servers.
- Sequence ID Tooltip (application only)
  This submenu's options allow the inclusion or exclusion of non-positional sequence features or database cross references from the tooltip shown when the mouse hovers over the sequence ID panel.
- Alignment Properties...
  Displays some simple statistics computed for the current alignment view and any named properties defined on the whole alignment.
- Overview Window
  A scaled version of the alignment will be displayed in a small window. A red box will indicate the currently visible area of the alignment. Move the visible region using the mouse.