X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=95904b6a18aa960e46a1c430fbe063c3ff7764bf;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=f95476f570eaa6111d7f1a4342e5a220b47bc0d6;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index f95476f..95904b6 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,12 +28,12 @@
   </p>
   <p>
     Trees are calculated on either the complete alignment, or just the
-    currently selected group of sequences, using the functions in the <strong>Calculate&#8594;Calculate
-      tree</strong> submenu. Once calculated, trees are displayed in a new <a
-      href="../calculations/treeviewer.html"
-    >tree viewing window</a>. There are four different calculations, using
-    one of two distance measures and constructing the tree from one of
-    two algorithms :
+    currently selected group of sequences, via the <a href="calculations.html">calculations dialog</a> opened from the <strong>Calculate&#8594;Calculate
+      Tree or PCA...</strong> menu entry. Once calculated, trees are displayed in a new <a
+      href="../calculations/treeviewer.html">tree viewing
+      window</a>. There are four different calculations, using one of two
+    distance measures and constructing the tree from one of two
+    algorithms :
   </p>
   <p>
     <strong>Distance Measures</strong>
@@ -56,8 +56,8 @@
       scores for the residue pairs at each aligned position.
       <ul>
         <li>For details about each model, see the <a
-          href="scorematrices.html"
-        >list of built-in score matrices</a>.
+          href="scorematrices.html">list of built-in score
+            matrices</a>.
         </li>
       </ul></li>
     <li><strong>Sequence Feature Similarity</strong><br>Trees
@@ -102,12 +102,12 @@
   </ul>
   <p>
     A newly calculated tree will be displayed in a new <a
-      href="../calculations/treeviewer.html"
-    >tree viewing window</a>. In addition, a new entry with the same tree
-    viewer window name will be added in the Sort menu so that the
-    alignment can be reordered to reflect the ordering of the leafs of
-    the tree. If the tree was calculated on a selected region of the
-    alignment, then the title of the tree view will reflect this.
+      href="../calculations/treeviewer.html">tree viewing
+      window</a>. In addition, a new entry with the same tree viewer window
+    name will be added in the Sort menu so that the alignment can be
+    reordered to reflect the ordering of the leafs of the tree. If the
+    tree was calculated on a selected region of the alignment, then the
+    title of the tree view will reflect this.
   </p>
 
   <p>
@@ -118,9 +118,9 @@
     phylogenetic trees, which can cope with large numbers of sequences,
     use better distance methods and can perform bootstrapping. Jalview
     can read <a
-      href="http://evolution.genetics.washington.edu/phylip/newick_doc.html"
-    >Newick</a> format tree files using the 'Load Associated Tree' entry
-    of the alignment's File menu. Sequences in the alignment will be
+      href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
+    format tree files using the 'Load Associated Tree' entry of the
+    alignment's File menu. Sequences in the alignment will be
     automatically associated to nodes in the tree, by matching Sequence
     IDs to the tree's leaf names.
   </p>
