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.
         </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
         <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
             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
               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,
             </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
             </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
             <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>
 
                 symbols will be rendered as a '.', highlighting
                 mutations in highly conserved alignments. </em></li>
 

-          </ul></li>

       </ul></li>
 
   </ul>
       </ul></li>
 
   </ul>

@@ -541,44 +540,26 @@
               viewer window.
           </em><br></li>
         </ul></li>
               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>
       </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
           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
                 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.
           </ul> Other sub-menus allow you to pick a specific source to query
           - sources are listed alphabetically according to their
           nickname.