new and corrected docs for 2.2 release

[jalview.git] / help / html / calculations / treeviewer.html

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index bc46771..f05572c 100755 (executable)
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -16,9 +16,15 @@
   are also reflected in any other analysis windows associated with the
   alignment, such as another tree viewer.</p>
 
-<p>
-  Clicking on an internal node of the tree will rearrange the tree
-  diagram, inverting the ordering of the branches at that node.
+<p>Moving the mouse over an internal node of the tree will highlight
+  it. You can then : <ul>
+  <li>Click the highlighted node to select all the sequences in that branch.
+  <li>Double-click the highlighted node to rearrange the tree
+  diagram by inverting the branch ordering at that
+  node.
+  <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
+  pick a new colour for the sub-tree and associated sequences.
+  </ul>
 </p>
 <p>
   Clicking anywhere along the extent of the tree (but not on a leaf or
@@ -47,12 +53,12 @@ retrieved with the 'Input Data...' entry.
 associated with a tree. Trees calculated by Jalview have branch
 lengths, which correspond to the distance measure used to construct
 the tree. Tree imported from outside may also contain bootstrap information,
-or additional leaves from sequences not present in the associated
+and additional leaves from sequences not present in the associated
 alignment.
 </p>
 <p>The view menu contains options controlling the way a tree is
-rendered and labelled:</p>
-<p><ul>
+rendered and labelled:
+<ul>
 <li><strong>Fit to Window</strong><p>
 The tree layout will be scaled to fit in the  display
 window. You may need to reduce the font size to minimise the leaf
@@ -70,8 +76,14 @@ Labels each branch or leaf with its associated bootstrap value.
 </p></li>
 <li><strong>Mark unlinked leaves</strong><p>
 Toggles the display of a '*' at the beginning of a leaf label to
-indicate that there is no sequence corresponding to that leaf in the associated alignment.
+indicate that there is no sequence corresponding to that leaf in the
+associated alignment.
 </p></li>
+<li><strong>Leaf Association</strong><p>
+Only visible when there are <a href="../features/multipleviews.html">multiple views</a> of the same
+alignment to show and edit which alignment views are associated with
+the leaves of the displayed tree.
+</p>
 </ul>
 </p>
 </body>