added the sorting entry to calculations, and corrected the PID

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

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index c61481f..a432824 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -17,8 +17,8 @@ precedence of their names.</p><p>
 <p>Places sequences in the same group adjacent to eachother.</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. 
+<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>
@@ -33,15 +33,12 @@ alignment, its name will appear in the submenu <em>Sort-&gt;By Tree Order</em>.<
 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>
+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>