6 <p><strong>Alignment Window Format Menu</strong></p>
8 <li><strong>Font...<br>
9 </strong><em>Opens the "Choose Font" dialog box, in order to
10 change the font of the display and enable or disable 'smooth fonts'
11 (anti-aliasing) for faster alignment rendering. </em></li>
13 </strong><em>When ticked, the alignment display is "<a
14 href="../features/wrap.html">wrapped</a>" to the width of the
15 alignment window. This is useful if your alignment has only a few
16 sequences to view its full width at once.<br>
17 Additional options for display of sequence numbering and scales are
18 also visible in wrapped layout mode:<br>
20 <li><strong>Scale Above</strong><br>Show the alignment column position scale.</li>
21 <li><strong>Scale Left</strong><br>Show the sequence position for the first aligned residue in each row in the left column of the alignment.</li>
22 <li><strong>Scale Right</strong><br>Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.</li>
24 <li><strong>Show Sequence Limits<br>
25 </strong><em>If this box is selected the sequence name will have the start
26 and end position of the sequence appended to the name, in the format
27 NAME/START-END</em></li>
28 <li><strong>Right Align Sequence ID<br>
29 </strong><em>If this box is selected then the sequence names displayed in
30 the sequence label area will be aligned against the left-hand edge of
31 the alignment display, rather than the left-hand edge of the alignment
33 <li><strong>Show Hidden Markers<br>
34 </strong><em>When this box is selected, positions in the alignment where
35 rows and columns are hidden will be marked by blue arrows.</li>
36 <li><strong>Boxes</strong><em><br>
37 If this is selected the background of a residue will be coloured using
38 the selected background colour. Useful if used in conjunction with
39 "Colour Text." </em></li>
41 </strong><em>If this is selected the residues will be displayed using the
42 standard 1 character amino acid alphabet.</em></li>
43 <li><strong>Colour Text<br>
44 </strong><em>If this is selected the residues will be coloured according to
45 the background colour associated with that residue. The colour is
46 slightly darker than background so the amino acid symbol remains
48 <li><strong>Show Gaps<br>
49 </strong><em>When this is selected, gap characters will be displayed as
50 "." or "-". If unselected, then gap characters will
51 appear as blank spaces. <br>
52 You may set the default gap character in <a
53 href="../features/preferences.html">preferences</a>.</em></li>