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 Text...</a></strong><em><br>
12 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.
14 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
15 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
16 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
17 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
18 a description of all colour schemes.</em><br>
20 <li><strong>By Conservation<br>
21 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
22 by Conservation</a>.</em><br>
24 <li><strong>Modify Conservation Threshold<br>
25 </strong><em>Use this to display the conservation threshold slider window.
26 Useful if the window has been closed, or if the 'by conservation' option
27 appears to be doing nothing!</em><br>
29 <li><strong>Above Identity Threshold<br>
30 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
31 Identity</a></em><strong>.<br>
33 <li><strong>Modify Identity Threshold<br>
34 </strong><em>Use this to set the threshold value for colouring above Identity.
35 Useful if the window has been closed.<br>
37 <li><strong>By Annotation</strong><br>
38 <em>Colours the alignment on a per-column value from a specified annotation.
39 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>