X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=d08f7136773375e2394860805041580d732a7087;hb=ff18d7ae4bedb6c79ab2e62032cf5f9a2bfedf6c;hp=80323487a675e09f4129dc01495e27b24ff97c01;hpb=dde303bc73617ab4eb3e681e67cf899e6a971318;p=jalview.git

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 8032348..d08f713 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -53,37 +53,19 @@
             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<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>Calculate Tree or PCA ...</strong> <br> <em>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>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 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 separated values in the description line of the
@@ -91,15 +73,17 @@
         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>Translate as cDNA</strong> (not applet)<br> <em>This
+    <li><strong>Translate as cDNA</strong><br> <em>This
         option is visible for nucleotide alignments. Selecting this
         option shows the DNA's calculated protein product in a new <a
         href="../features/splitView.html">split frame</a> window. Note
         that the translation is not frame- or intron-aware; it simply
-        translates all codons in each sequence, using the standard <a
-        href="../misc/geneticCode.html">genetic code</a> (any incomplete
-        final codon is discarded). You can perform this action on the
-        whole alignment, or selected rows, columns, or regions.
+        translates all codons in each sequence. You can use the standard <a
+        href="../misc/geneticCode.html">genetic code</a>, or choose an 
+        alternative code table (any incomplete final codon is discarded). 
+        You can perform this action on the whole alignment, or selected 
+        rows, columns, or regions. Alternative code tables were added in
+        Jalview 2.11.
     </em> <br></li>
     <li><strong>Reverse, Reverse Complement</strong> (not applet)<br>
       <em>These options are visible for nucleotide alignments.