2 <head><title>Alignment Window Menus</title></head>
5 <p><strong>Alignment Window Colour Menu</strong></p>
7 <li><strong>Apply Colour To All Groups<br>
8 </strong><em>If this is selected, any changes made to the background colour
9 will be applied to all currently defined groups.<br>
11 <li><strong><a href="../colourSchemes/textcolour.html">Colour
12 Text ...</a></strong><em><br>
13 Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
15 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
16 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
17 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
18 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
19 a description of all colour schemes.</em><br>
21 <li><strong>By Conservation<br>
22 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
23 by Conservation</a>.</em><br>
25 <li><strong>Modify Conservation Threshold<br>
26 </strong><em>Use this to display the conservation threshold slider window.
27 Useful if the window has been closed, or if the 'by conservation' option
28 appears to be doing nothing!</em><br>
30 <li><strong>Above Identity Threshold<br>
31 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
32 Identity</a></em><strong>.<br>
34 <li><strong>Modify Identity Threshold<br>
35 </strong><em>Use this to set the threshold value for colouring above Identity.
36 Useful if the window has been closed.<br>
38 <li><strong>By Annotation</strong><br>
39 <em>Colours the alignment on a per-column value from a specified annotation.
40 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>