Alignment Window Menus
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 Above
Show the alignment column position scale.
- 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.
- 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.