<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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>Sorting Sequences</title>
</head>
<p><strong>Sorting Sequences</strong></p>
<p>Any group of selected sequences may be reordered by pressing the
up or down arrow keys. The whole alignment may also be reordered by
-the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
+the use of the functions in the Sort menu (<strong>Calculate→Sort</strong>):
</p>
<ul>
<li><p><strong>Sort by ID</strong></p>
precedence of their names.</p><p>
</li>
<li><p><strong>Sort by Group</strong></p>
-<p>Places sequences in the same group adjacent to eachother.</p><p>
+<p>Places sequences in the same group adjacent to each other.</p><p>
</li>
<li><p><strong>Sort by Pairwise Identity</strong></p>
<p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues.
+fraction of conserved residues.
</p><p>
</li>
<li><p><strong>Sort by Tree Order</strong></p>
order the sequences corresponding to those leaves in the
alignment.<br>
If a tree has been calculated from or associated with the current
-alignment, its name will appear in the submenu <em>Sort->By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort→By Tree Order</strong>.</p><p>
</li>
<li><p><strong>Sort by alignment ordering</strong></p>
<p>Multiple alignment methods often order the sequences in their
If the current alignment has been generated by one of Jalview's
alignment web services, the alignment ordering can be recovered by
its corresponding entry in the Sort menu.
-</p><p>
+</p>
</li>
+<li><p><strong>Sort by Score</strong></p>
+<p>This menu appears if the alignment contains any <a href="../features/annotationsFormat.html">sequence associated
+alignment annotation</a> with associated score values. Each entry is the
+label for a distinct group of sequence associated annotation
+scores which can be used for sorting.</p>
</ul>
<p><strong>Reversing the Order</strong></p>
<p>Selecting any item from the Sort menu will sort sequences in an