3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Alignment Window Menus</title>
28 <strong>Alignment Window Colour Menu</strong>
31 <li><strong>Apply Colour To All Groups<br>
32 </strong><em>If this is selected, any changes made to the background
33 colour will be applied to all currently defined groups.<br>
35 <li><strong><a href="../colourSchemes/textcolour.html">Colour
36 Text ...</a></strong><em><br> Opens the Colour Text dialog box to
37 set a different text colour for light and dark background, and
38 the intensity threshold for transition between them. </em></li>
39 <li>Colour Scheme options: <strong>None, ClustalX,
40 Blosum62 Score, Percentage Identity, Zappo, Taylor,
41 gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
42 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
43 Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
45 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
46 a description of all colour schemes.
49 <li><strong>Sequence ID<br></strong><em>Shades
50 sequences using their Sequence ID colour. Useful when performing
51 <a href="../calculations/treeviewer.html#partitioning">tree
52 based subfamily analysis</a>.
54 <li><strong>By Conservation<br>
55 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
58 <li><strong>Modify Conservation Threshold<br>
59 </strong><em>Use this to display the conservation threshold slider
60 window. Useful if the window has been closed, or if the 'by
61 conservation' option appears to be doing nothing!</em><br></li>
62 <li><strong>Above Identity Threshold<br>
63 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
64 Percentage Identity</a></em><strong>.<br>
66 <li><strong>Modify Identity Threshold<br>
67 </strong><em>Use this to set the threshold value for colouring above
68 Identity. Useful if the window has been closed.<br>
70 <li><strong>By Annotation</strong><br> <em>Colours
71 the alignment on a per-column value from a specified annotation.
72 See <a href="../colourSchemes/annotationColouring.html">Annotation
75 <li><strong>By RNA Helices</strong><br> <em>Colours
76 the helices of an RNA alignment loaded from a Stockholm file.
77 See <a href="../colourSchemes/rnahelicesColouring.html">RNA
78 Helices Colouring</a>.