3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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22 <head><title>Alignment Window Menus</title></head>
25 <p><strong>Alignment Window Colour Menu</strong></p>
27 <li><strong>Apply Colour To All Groups<br>
28 </strong><em>If this is selected, any changes made to the background colour
29 will be applied to all currently defined groups.<br>
31 <li><strong><a href="../colourSchemes/textcolour.html">Colour
32 Text ...</a></strong><em><br>
33 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.
35 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
36 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
37 Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
38 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
39 a description of all colour schemes.</em><br>
41 <li><strong>By Conservation<br>
42 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
43 by Conservation</a>.</em><br>
45 <li><strong>Modify Conservation Threshold<br>
46 </strong><em>Use this to display the conservation threshold slider window.
47 Useful if the window has been closed, or if the 'by conservation' option
48 appears to be doing nothing!</em><br>
50 <li><strong>Above Identity Threshold<br>
51 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
52 Identity</a></em><strong>.<br>
54 <li><strong>Modify Identity Threshold<br>
55 </strong><em>Use this to set the threshold value for colouring above Identity.
56 Useful if the window has been closed.<br>
58 <li><strong>By Annotation</strong><br>
59 <em>Colours the alignment on a per-column value from a specified annotation.
60 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
62 <li><strong>By RNA Helices</strong><br>
63 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
64 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
65 Colouring</a>.</em><br>