<html>
-<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>Grouping sequences by partitioning the tree at a particular distanec</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>.</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 contains options controlling the way a tree is
-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
-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>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>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
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