--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+ <p>
+ <strong>Alignment Window Colour Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Apply Colour To All Groups<br>
+ </strong><em>If this is selected, any changes made to the background
+ colour will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour
+ Text ...</a></strong><em><br> 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. </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX,
+ Blosum62 Score, Percentage Identity, Zappo, Taylor,
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
+ a description of all colour schemes.
+ </em><br>
+ </li>
+ <li><strong>Sequence ID<br></strong><em>Shades
+ sequences using their Sequence ID colour. Useful when performing
+ <a href="../calculations/treeviewer.html#partitioning">tree
+ based subfamily analysis</a>.
+ </em></li>
+ <li><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.
+ </em><br></li>
+ <li><strong>Modify Conservation Threshold<br>
+ </strong><em>Use this to display the conservation threshold slider
+ window. Useful if the window has been closed, or if the 'by
+ conservation' option appears to be doing nothing!</em><br></li>
+ <li><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above
+ Percentage Identity</a></em><strong>.<br>
+ </strong></li>
+ <li><strong>Modify Identity Threshold<br>
+ </strong><em>Use this to set the threshold value for colouring above
+ Identity. Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br> <em>Colours
+ the alignment on a per-column value from a specified annotation.
+ See <a href="../colourSchemes/annotationColouring.html">Annotation
+ Colouring</a>.
+ </em><br></li>
+ <li><strong>By RNA Helices</strong><br> <em>Colours
+ the helices of an RNA alignment loaded from a Stockholm file.
+ See <a href="../colourSchemes/rnahelicesColouring.html">RNA
+ Helices Colouring</a>.
+ </em><br></li>
+ </ul>
+</body>
+</html>