X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=eb51c6268c863274f4a9454840c36820ee9e9fd7;hb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;hp=d6bd77eda836226e61a547889105e4ec4f12c000;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d6bd77e..eb51c62 100755
--- 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
@@ -287,9 +287,13 @@
 						<li><strong>Show Consensus Histogram<br> </strong><em>
 							Enable or disable the display of the histogram above the
 							consensus sequence.</em></li>
-						<li><strong>Show Consensus Profile<br> </strong><em> Enable
-							or disable the display of the sequence logo above the consensus
+						<li><strong>Show Consensus Logo<br> </strong><em> Enable
+							or disable the display of the Consensus Logo above the consensus
 							sequence.</em></li>
+						<li><strong>Normalise Consensus Logo<br>
+						</strong><em>When enabled, scales all logo stacks to the same height,
+								making it easier to compare symbol diversity in highly variable
+								regions.</em></li>
 						<li><strong>Group Conservation<br> </strong><em> When
 							ticked, display a conservation row for all groups (only available
 							for protein alignments).</em></li>
@@ -391,6 +395,9 @@
 
 					</ul></li>
 			</ul>
+	</li>
+
+		</ul>
 		</li>
 
 		<li><strong>Colour</strong>
@@ -407,7 +414,7 @@
 				<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 +436,11 @@
 						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>
@@ -553,10 +565,10 @@
 					</ul></li>
 				<li><strong>Analysis</strong><br />
 					<ul>
-						<li><strong>Sequence Harmony Multi-Relief</strong><br> <em>Performs
+						<li><strong>Multi-Harmony</strong><br> <em>Performs
 								functional residue analysis on a protein family alignment with
 								sub-families defined on it. See the <a
-								href="../webServices/shmr.html">SHMR client</a> entry for more
+								href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
 								information.</em>
 						</li>
 					</ul></li>
