Alignment Window Format Menu

- Font...
  Opens the "Choose Font" dialog box, in order to change the font of the display and enable or disable 'smooth fonts' (anti-aliasing) for faster alignment rendering.
- Wrap
  When ticked, the alignment display is "wrapped" to the width of the alignment window. This is useful if your alignment has only a few sequences to view its full width at once.
  Additional options for display of sequence numbering and scales are also visible in wrapped layout mode:
  - Scale Left
    Show the sequence position for the first aligned residue in each row in the left column of the alignment.
  - Scale Right
    Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.
  - Scale Above
    Show the alignment column position scale.
- Show Sequence Limits
  If this box is selected the sequence name will have the start and end position of the sequence appended to the name, in the format NAME/START-END
- Right Align Sequence ID
  If this box is selected then the sequence names displayed in the sequence label area will be aligned against the left-hand edge of the alignment display, rather than the left-hand edge of the alignment window.
- Show Hidden Markers
  When this box is selected, positions in the alignment where rows and columns are hidden will be marked by blue arrows.
- Boxes
  If this is selected the background of a residue will be coloured using the selected background colour. Useful if used in conjunction with "Colour Text."
- Text
  If this is selected the residues will be displayed using the standard 1 character amino acid alphabet.
- Colour Text
  If this is selected the residues will be coloured according to the background colour associated with that residue. The colour is slightly darker than background so the amino acid symbol remains visible.
- Show Gaps
  When this is selected, gap characters will be displayed as "." or "-". If unselected, then gap characters will appear as blank spaces.
  You may set the default gap character in preferences.
- Centre Column Labels
  When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
- Show Unconserved
  When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.