X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;fp=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=a1c630e5e12d837794cf4e316076e31d1798e2c1;hb=de255c8c87707a2cd2a2a15f5ad04ed10fe5846d;hp=10b5611d8a8f938695115feb299d857cf3c35483;hpb=d924d4634167f98c9fd94df6714a6589c1368da3;p=jalview.git

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 10b5611..a1c630e 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -30,20 +30,20 @@
 	<ul>
 		<li><strong>Sort </strong>
 			<ul>
-				<li><strong>by ID</strong><em><br> This will sort the
+				<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
+				<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
+				<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. </em><strong></strong>
 				</li>
-				<li><strong>by Pairwise Identity<br> </strong><em>This
+				<li><strong>By Pairwise Identity<br> </strong><em>This
 						will sort the selected sequences by their percentage identity to
 						the consensus sequence. The most similar sequence is put at the
 						top. </em>
@@ -53,28 +53,32 @@
 						associated score annotation, or you have just done a multiple
 						alignment calculation or opened a tree viewer window.</em><br></li>
 			</ul></li>
-		<li><strong>Calculate Tree </strong> <br> <em>Functions
-				for calculating trees on the alignment or the currently selected
-				region. See <a href="../calculations/tree.html">calculating
-					trees</a>.</em>
-			<ul>
-				<li><strong>Average Distance Using % Identity</strong>
-				</li>
-				<li><strong>Neighbour Joining Using % Identity</strong>
-				</li>
-				<li><strong>Average Distance Using Blosum62</strong>
-				</li>
-				<li><strong>Neighbour Joining Using Blosum62<br>
-				</strong>
-				</li>
-			</ul></li>
-		<li><strong>Pairwise Alignments</strong><br> <em>Applies
+    <li><strong>Calculate Tree </strong> <br> <em>Functions
+        for calculating trees on the alignment or the currently selected
+        region. See <a href="../calculations/tree.html">calculating
+          trees</a>.
+    </em>
+      <ul>
+        <li><strong>Neighbour Joining Using PAM250<br>
+        </strong></li>
+        <li><strong>Neighbour Joining Using Sequence
+            Feature Similarity</strong></li>
+        <li><strong>Neighbour Joining Using Blosum62<br>
+        </strong></li>
+        <li><strong>Neighbour Joining Using % Identity</strong></li>
+        <li><strong>Average Distance Using PAM250<br>
+        </strong></li>
+        <li><strong>Average Distance Using Sequence
+            Feature Similarity</strong></li>
+        <li><strong>Average Distance Using Blosum62</strong></li>
+        <li><strong>Average Distance Using % Identity</strong></li>
+      </ul></li>
+    <li><strong>Pairwise Alignments</strong><br> <em>Applies
 				Smith and Waterman algorithm to selected sequences. See <a
 				href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
 		</li>
 		<li><strong>Principal Component Analysis</strong><br> <em>Shows
-				a spatial clustering of the sequences based on the BLOSUM62 scores
-				in the alignment. See <a href="../calculations/pca.html">Principal
+				a spatial clustering of the sequences based on similarity scores calculated over 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
@@ -99,6 +103,12 @@
 				this option is selected, the alignment will be automatically sorted
 				whenever a new tree is calculated or loaded.</em> <br>
 		</li>
-	</ul>
+    <li><strong>Show Flanking Regions</strong><br> <em>Opens
+        a new alignment window showing any additional sequence data
+        either side of the current alignment. Useful in conjunction with
+        'Fetch Database References' when the 'Trim Retrieved Sequences'
+        option is disabled to retrieve full length sequences for a set
+        of aligned peptides. </em></li>
+  </ul>
 </body>
 </html>