3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>The Tree Viewing Window</title>
26 <p><strong>The Tree Viewing Window</strong></p>
28 The tree viewing window is opened when a tree has been <a href="tree.html">calculated
29 from an alignment</a>, or imported via a file or web service. It includes <a href="#menus">menus</a> for
30 controlling layout and file and figure creation, and enables
31 various selection and colouring operations on the
32 associated sequences in the alignment.</p>
34 <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
35 Selecting sequence ids at the leaves of the tree selects the
36 corresponding sequences in the original alignment. These selections
37 are also reflected in any other analysis windows associated with the
38 alignment, such as another tree viewer.</p>
39 <p><strong><em>Grouping sequences by partitioning the tree at a particular distanec</em></strong><br>
40 Clicking anywhere along the extent of the tree (but not on a leaf or
41 internal node) defines a tree 'partition', by cutting every branch
42 of the tree spanning the depth where the mouse-click occurred. Groups
43 are created containing sequences at the leaves of each connected
44 sub tree. These groups are each given a different colour, which are
45 reflected in other windows in the same way as if the sequence ids
46 were selected, and can be edited in the same way as user defined
49 <p>Tree partitions are useful for comparing clusters produced by
50 different methods and measures. They are also an effective way of
51 identifying specific patterns of conservation and mutation
52 corresponding to the overall phylogenetic structure, when combined
53 with the <a href="../colourSchemes/conservation.html">conservation
54 based colour scheme</a>.</p>
56 <strong><em>Selecting Subtrees and changing the branch order and subtree group colour</em></strong><br>
57 Moving the mouse over an internal node of the tree will highlight
58 it. You can then : <ul>
59 <li>Click the highlighted node to select all the sequences in that branch.
60 <li>Double-click the highlighted node to rearrange the tree
61 diagram by inverting the branch ordering at that
63 <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
64 pick a new colour for the sub-tree and associated sequences.
67 <p><strong><a name="menus">
68 File Menu</a></strong></p>
69 <p>This menu allows the displayed tree to be saved as a Newick tree
70 file (Save→Newick File), printed or exported as an image (PNG) or
71 Postscript file. Finally, data used to calculate the tree can be
72 retrieved with the 'Input Data...' entry.
74 <p><strong>View Menu</strong></p>
75 <p>When the tree viewer is opened, it displays all the annotation
76 associated with a tree. Trees calculated by Jalview have branch
77 lengths, which correspond to the distance measure used to construct
78 the tree. Tree imported from outside may also contain bootstrap information,
79 and additional leaves from sequences not present in the associated
82 <p>The view menu mostly contains options controlling the way a tree is
85 <li><strong>Fit to Window</strong><p>
86 The tree layout will be scaled to fit in the display
87 window. You may need to reduce the font size to minimise the leaf
88 label overlap when this option is selected.
90 <li><strong>Font Size ...</strong><em>n</em><p>
91 Brings up a dialog box to set the font size for the leaf
92 names. <em>n</em> is the current font size.
94 <li><strong>Show Distances</strong><p>
95 Labels each branch or leaf with its associated branch
97 <li><strong>Show Bootstrap values</strong><p>
98 Labels each branch or leaf with its associated bootstrap value.
100 <li><strong>Mark unlinked leaves</strong><p>
101 Toggles the display of a '*' at the beginning of a leaf label to
102 indicate that there is no sequence corresponding to that leaf in the
103 associated alignment.
105 <li><strong>Sort Alignment By Tree</strong>
107 Sorts any associated alignment views using the current tree. (<em>Only
108 available in the Jalview Desktop</em>)
111 <li><strong>Associate Leaves with ...</strong>
113 Only visible when there are <a href="../features/multipleviews.html">multiple
114 views</a> of the same alignment to show and edit which alignment views
115 are associated with the leaves of the displayed tree.