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

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 0d605f8..a432824 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -6,41 +6,39 @@
 <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 (Calculate->Sort):
+the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
 </p>
 <ul>
-<li><strong>Sort by ID</strong>
+<li><p><strong>Sort by ID</strong></p>
 <p>Orders the sequences by the alphanumeric (0-9A-Za-z)
-precedence of their names.</p>
+precedence of their names.</p><p>
 </li>
-<li><strong>Sort by Group</string>
-<p>Places sequences in the same group adjacent to eachother.</p>
+<li><p><strong>Sort by Group</strong></p>
+<p>Places sequences in the same group adjacent to eachother.</p><p>
 </li>
-<li><strong>Sort by Pairwise Identity</strong> 
-<p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues. 
-</p>
-</li><strong>Sort by Tree Order</strong>
+<li><p><strong>Sort by Pairwise Identity</strong></p>
+<p>Sequences are ordered by decreasing fraction of conserved residues
+with respect to the first sequence in the alignment.
+</p><p>
+</li>
+<li><p><strong>Sort by Tree Order</strong></p>
 <p>The leaf ordering of a particular phylogenetic tree is used to
 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 'Sort->By Tree Order->'.<p>
+alignment, its name will appear in the submenu <em>Sort-&gt;By Tree Order</em>.</p><p>
 </li>
-<li><strong>Sort by alignment ordering</strong>
+<li><p><strong>Sort by alignment ordering</strong></p>
 <p>Multiple alignment methods often order the sequences in their
 alignments by some measure of sequence identity.<br>
-If the current alignment has been generated by one of the Jalview
+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->By ..' menu.
-</p>
+its corresponding entry in the Sort menu:
 </li>
 </ul>
-<p><strong>Reversing the Order</strong></p>
-<p>Selecting any item from the Sort menu will sort sequences in an
-ascending order according to the property defining the sort. If the
-same sort is re-applied, the sequences will be sorted in the inverse
-order. In the case of trees and alignment orderings, Jalview will
+<strong>Reversing the Order</strong>
+<p>If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse
+order for that property. In the case of trees and alignment orderings, Jalview will
 remember your last choice for sorting the alignment and only apply the
 inverse ordering if you select the same tree or alignment ordering
 item again.</p>