-<p></p>\r
-<p><strong>The Tree Viewing Window</strong></p>\r
-<p>\r
- When the tree has been calculated a window is displayed showing the\r
- tree, with the leaves labelled with sequence ids. \r
-<p>Selecting the 'show distances' checkbox will put branch lengths on the branches.\r
- These branch lengths are the percentage mismatch between two nodes. </p>\r
- \r
-<p>\r
- Selecting sequence ids at the leaves of the tree selects sequences\r
- in the original alignment. These selections are reflected in any\r
- other analysis windows open on the same alignment. </p>\r
-<p>\r
- Clicking on an internal node of the tree will rearrange the tree\r
- diagram, inverting the ordering of the branches at that node.\r
-</p>\r
-<p>\r
- Clicking anywhere along the extent of the tree (but not on a leaf or\r
- internal node) defines a tree 'partition', by cutting every branch\r
- of the tree spanning the depth where the mouse-click occured. Groups\r
- are created containing sequences at the leaves of each connected\r
- subtree. These groups are each given a different colour, which are\r
- reflected in other windows in the same way as if the sequence ids\r
- were selected, and can be edited in the same way as user defined\r
- sequence groups.\r
-</p>\r
-<p>Tree partitions are useful for comparing clusterings produced by\r
-different methods and measures. They are also an effective way of\r
-identifying specific patterns of conservation and mutation\r
-corresponding to the overall phylogenetic structure, when combined\r
-with the <a href="../colourSchemes/conservation.html">conservation\r
-based colour scheme</a>.</p>\r
+<p>A newly calculated tree will be displayed in a new <a\r
+href="../calculations/treeviewer.html">tree viewing window</a>. In\r
+addition, a new entry with the same tree viewer window name will be added in the Sort\r
+menu so that the alignment can be reordered to reflect the ordering of\r
+the leafs of the tree. If the tree was calculated on a selected region\r
+of the alignment, then the title of the tree view will reflect this.</p>\r