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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
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* This file is part of Jalview.
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* 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.
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+ *
* 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.
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* 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.
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+<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 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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