JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes

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

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 51ad601..00a2ec4 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -244,7 +244,7 @@
         </strong><em>Selects all the sequences and residues in the
             alignment. <br> Use &lt;CTRL&gt; and A (&lt;APPLE&gt;
             and A on a MacOSX) to select all.
-        </em></em></li>
+        </em></li>
         <li><strong>Deselect All (Escape)<br>
         </strong><em>Removes the current selection box (red dashed box) from
             the alignment window. All selected sequences, residues and
@@ -312,7 +312,7 @@
             or hide sequence features on this alignment.</em></li>
         <li><strong><a
             href="../features/featuresettings.html">Sequence
-              Feature Settings...</a> </strong><em><br> <em>Opens the
+              Feature Settings...</a> </strong><br> <em>Opens the
               Sequence Feature Settings dialog box to control the colour
               and display of sequence features on the alignment, and
               configure and retrieve features from DAS annotation
@@ -427,12 +427,12 @@
             </strong><em>If this box is selected then the sequence names
                 displayed in the sequence label area will be aligned
                 against the left-hand edge of the alignment display,
-                rather than the left-hand edge of the alignment window.
+                rather than the left-hand edge of the alignment window.</em>
             </li>
             <li><strong>Show Hidden Markers<br>
             </strong><em>When this box is selected, positions in the
                 alignment where rows and columns are hidden will be
-                marked by blue arrows. </li>
+                marked by blue arrows. </em></li>
             <li><strong>Boxes</strong><em><br> If this is
                 selected the background of a residue will be coloured
                 using the selected background colour. Useful if used in
@@ -461,7 +461,6 @@
                 symbols will be rendered as a '.', highlighting
                 mutations in highly conserved alignments. </em></li>
 
-          </ul></li>
       </ul></li>
 
   </ul>
@@ -541,44 +540,26 @@
               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>Neighbour Joining Using PAM250 </strong></li>
-          <li><strong>Neighbour Joining Using Sequence
-              Feature Similarity</strong></li>
-          <li><strong>Neighbour Joining Using Blosum62 </strong></li>
-          <li><strong>Neighbour Joining Using % Identity</strong></li>
-          <li><strong>Average Distance Using PAM250 </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> <strong>Note: Since Version 2.8.1, a number of
-          additional similarity measures for tree calculation are
-          provided in this menu.</strong></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>.
+    <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the 
+    <a href="../calculations/calculations.html">calculations dialog</a> for
+        for calculating <a href="../calculations/tree.html">trees</a> or
+         <a href="../calculations/pca.html">principle component analysis 
+         plots</a> on the alignment or the currently selected
+        region. 
       </em><br></li>
-      <li><strong>Principal Component Analysis</strong><br> <em>Shows
-          a spatial clustering of the sequences based on similarity
-          scores calculated with 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 separated values in the description line of the
-          alignment sequences.<br> When selected, these numbers are
-          parsed into sequence associated annotation which can then be
-          used to sort the alignment via the Sort by&#8594;Score menu.
-      </em> <br></li>
-      <li><strong>Autocalculate Consensus</strong><br> <em>For
+    <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>Extract Scores ... (optional)</strong><br> <em>This
+        option is only visible if Jalview detects one or more
+        white-space separated values in the description line of the
+        alignment sequences.<br> When selected, these numbers are
+        parsed into sequence associated annotation which can then be
+        used to sort the alignment via the Sort by&#8594;Score menu.
+    </em> <br></li>
+    <li><strong>Autocalculate Consensus</strong><br> <em>For
           large alignments it can be useful to deselect
           &quot;Autocalculate Consensus&quot; when editing. This
           prevents the sometimes lengthy calculations performed after
@@ -614,7 +595,7 @@
                 in Jalview 2.8.1</strong>
             </li>
             <li>'Standard Databases' will check sequences against
-              the EBI databases plus any active DAS sequence sources<</li>
+              the EBI databases plus any active DAS sequence sources</li>
           </ul> Other sub-menus allow you to pick a specific source to query
           - sources are listed alphabetically according to their
           nickname.