<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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>Annotation Panel Menus</title>
</head>
This is useful to export alignment quality measurements for further analysis.</em>
</li>
</ul>
- <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
+ <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em>
<ul>
+
<li><strong>Ignore Gaps in Consensus</strong><br>
If this checkbox is selected, all consensus calculations performed in
the current Alignment window will be done without counting gaps as a consensus
character.</li>
+ <li><strong>Show Consensus Histogram<br></strong>
+ Enable or disable the display of the histogram above the consensus sequence.
+ </li>
+ <li>
+ <strong>Show Consensus Logo<br></strong>
+ Enable or disable the display of the sequence logo above the consensus sequence.
+ </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>
<li><strong>Copy Consensus Sequence</strong><br>
Copies the consensus sequence to the clipboard in Fasta format, to allow
the consensus sequence to be added to an alignment. Note the copied sequence