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.
- Show Unconserved
When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
- 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.