JAL-1645 yet more documentation tweaks

[jalview.git] / help / html / menus / alwcalculate.html

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 10b5611..a1c630e 100755 (executable)
--- 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>