InstallAnywhere 2009

[jalview.git] / help / html / calculations / sorting.html

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index c61481f..1c15890 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -6,7 +6,7 @@
 <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&#8594;Sort</strong>):
 </p>
 <ul>
 <li><p><strong>Sort by ID</strong></p>
@@ -14,11 +14,11 @@ the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
 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>
@@ -26,7 +26,7 @@ fraction of conserved residues.
 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-&gt;By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort&#8594;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
@@ -34,8 +34,13 @@ alignments by some measure of sequence identity.<br>
 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