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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
<head><title>Alignment Window Menus</title></head>
<body>
<li><strong>by ID</strong><em><br>
This will sort the sequences according to sequence name. If the sort is
repeated, the order of the sorted sequences will be inverted. </em></li>
+ <li><strong>by Length</strong><em><br>
+ This will sort the sequences according to their length (excluding gap characters). If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em></li>
<li><strong>by Group</strong><strong><br>
</strong><em>This will sort the sequences according to sequence name.
If the sort is repeated, the order of the sorted sequences will be inverted.
identity to the consensus sequence. The most similar sequence is put at
the top. </em></li>
<li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have
- some additional options if you have just done a multiple alignment calculation,
+ some additional options if the alignment has any associated
+ score annotation, or you have just done a multiple alignment calculation
or opened a tree viewer window.</em><br>
</li>
</ul>
in the alignment. See <a href="../calculations/pca.html">Principal Component
Analysis</a>.</em> <br>
</li>
+ <li><strong>Extract Scores ... (optional)</strong><br>
+ <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
+ When selected, these numbers are parsed into sequence associated annotation which can
+ then be used to sort the alignment via the Sort by→Score menu.</em> <br>
+ </li>
+
<li><strong>Autocalculate Consensus</strong><br>
<em>For large alignments it can be useful to deselect "Autocalculate
Consensus" when editing. This prevents the sometimes lengthy calculations