Merge branch 'feature/JAL-3181linkOrdering' into develop

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

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index b45f8fe..8cb2b59 100755 (executable)
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -28,29 +28,28 @@
   </p>
   <p>
     The tree viewing window is opened when a tree has been <a
-      href="tree.html"
-    >calculated from an alignment</a>, or imported via a file or web
-    service. It includes <a href="#menus">menus</a> for controlling
-    layout and file and figure creation, and enables various selection
-    and colouring operations on the associated sequences in the
-    alignment.
+      href="tree.html">calculated from an alignment</a>, or
+    imported via a file or web service. It includes <a href="#menus">menus</a>
+    for controlling layout and file and figure creation, and enables
+    various selection and colouring operations on the associated
+    sequences in the alignment.
   </p>
   <p>
     <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
-    Selecting sequence ids at the leaves of the tree selects the
+    Selecting sequence IDs at the leaves of the tree selects the
     corresponding sequences in the original alignment. These selections
     are also reflected in any other analysis windows associated with the
     alignment, such as another tree viewer.
   </p>
   <p>
-    <strong><em>Grouping sequences by partitioning the
-        tree at a particular distanec</em></strong><br> Clicking anywhere along
+    <strong><em><a name="partitioning">Grouping sequences by partitioning</a> the
+        tree at a particular distance</em></strong><br> Clicking anywhere along
     the extent of the tree (but not on a leaf or internal node) defines
     a tree 'partition', by cutting every branch of the tree spanning the
     depth where the mouse-click occurred. Groups are created containing
     sequences at the leaves of each connected sub tree. These groups are
     each given a different colour, which are reflected in other windows
-    in the same way as if the sequence ids were selected, and can be
+    in the same way as if the sequence IDs were selected, and can be
     edited in the same way as user defined sequence groups.
   </p>
   <p>
@@ -59,7 +58,10 @@
     identifying specific patterns of conservation and mutation
     corresponding to the overall phylogenetic structure, when combined
     with the <a href="../colourSchemes/conservation.html">conservation
-      based colour scheme</a>.
+      based colour scheme</a>.To distinguish parts of the alignment assigned
+    to different groups, you may also enable the Sequence ID colour
+    scheme via the <a href="../menus/alwcolour.html">Alignment
+      window's Colours menu</a> (<em>Since 2.11</em>).
   </p>
   <p>
     <strong><em>Selecting Subtrees and changing the branch
@@ -95,23 +97,24 @@
     tree is rendered and labeled:
   <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 label
-        overlap when this option is selected.</p></li>
+      <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 label overlap when this option is selected.</p></li>
     <li><strong>Font Size ...</strong><em>n</em>
-    <p>
+      <p>
         Brings up a dialog box to set the font size for the leaf names.
         <em>n</em> is the current font size.
       </p></li>
     <li><strong>Show Distances</strong>
-    <p>Labels each branch or leaf with its associated branch length.</p></li>
+      <p>Labels each branch or leaf with its associated branch
+        length.</p></li>
     <li><strong>Show Bootstrap values</strong>
-    <p>Labels each branch or leaf with its associated bootstrap
+      <p>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.</p></li>
+      <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.</p></li>
     <li><strong>Sort Alignment By Tree</strong>
       <p>
         Sorts any associated alignment views using the current tree. (<em>Only
@@ -120,10 +123,9 @@
     <li><strong>Associate Leaves with ...</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.
+          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>