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update author list in license for (JAL-826)
[jalview.git] / help / html / menus / alignmentMenu.html
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ff74139..4a1a200 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -28,8 +28,8 @@
                <li><strong>File</strong>
                        <ul>
                                <li><strong>Fetch Sequence</strong><br> <em>Shows a
-                                               dialog window in which you can select known ids from Uniprot,
-                                               EMBL, EMBLCDS or PDB database using Web Services provided by the
+                                               dialog window in which you can retrieve known ids from Uniprot,
+                                               EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
                                                European Bioinformatics Institute. See <a
                                                href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
                                <li><strong>Add Sequences</strong><em><br> Add
@@ -391,6 +391,9 @@
 
                                        </ul></li>
                        </ul>
+       </li>
+
+               </ul>
                </li>
 
                <li><strong>Colour</strong>
@@ -407,7 +410,7 @@
                                <li>Colour Scheme options: <strong>None, ClustalX,
                                                Blosum62 Score, Percentage Identity, Zappo, Taylor,
                                                Hydrophobicity, Helix Propensity, Strand Propensity, Turn
-                                               Propensity, Buried Index, Nucleotide, User Defined<br> </strong> <em>See
+                                               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>By Conservation<br> </strong><em>See <a
@@ -429,6 +432,11 @@
                                                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></li>
                <li><strong>Calculate</strong>
                        <ul>