--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Tree Viewing Window</title>
+</head>
+<body>
+ <p>
+ <strong>The Tree Viewing Window</strong>
+ </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.
+ </p>
+ <p>
+ <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
+ 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><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
+ edited in the same way as user defined sequence groups.
+ </p>
+ <p>
+ Tree partitions are useful for comparing clusters produced by
+ different methods and measures. They are also an effective way of
+ 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>.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
+ order and subtree group colour</em></strong><br> 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>
+ <strong><a name="menus"> File Menu</a></strong>
+ </p>
+ <p>This menu allows the displayed tree to be saved as a Newick
+ tree file (Save→Newick File), printed or exported as an image
+ (PNG) or Postscript file. Finally, data used to calculate the tree
+ can be retrieved with the 'Input Data...' entry.</p>
+ <p>
+ <strong>View Menu</strong>
+ </p>
+ <p>When the tree viewer is opened, it displays all the annotation
+ 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, and additional leaves from sequences not present in the
+ associated alignment.</p>
+ <p>The view menu mostly contains options controlling the way a
+ 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>
+ <li><strong>Font Size ...</strong><em>n</em>
+ <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>
+ <li><strong>Show Bootstrap values</strong>
+ <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>
+ <li><strong>Sort Alignment By Tree</strong>
+ <p>
+ Sorts any associated alignment views using the current tree. (<em>Only
+ available in the Jalview Desktop</em>)
+ </p></li>
+ <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.
+ </p>
+ </ul>
+ </p>
+</body>
+</html>
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