3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>The Tree Viewing Window</title>
27 <strong>The Tree Viewing Window</strong>
30 The tree viewing window is opened when a tree has been <a
32 >calculated from an alignment</a>, or imported via a file or web
33 service. It includes <a href="#menus">menus</a> for controlling
34 layout and file and figure creation, and enables various selection
35 and colouring operations on the associated sequences in the
39 <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
40 Selecting sequence ids at the leaves of the tree selects the
41 corresponding sequences in the original alignment. These selections
42 are also reflected in any other analysis windows associated with the
43 alignment, such as another tree viewer.
46 <strong><em>Grouping sequences by partitioning the
47 tree at a particular distanec</em></strong><br> Clicking anywhere along
48 the extent of the tree (but not on a leaf or internal node) defines
49 a tree 'partition', by cutting every branch of the tree spanning the
50 depth where the mouse-click occurred. Groups are created containing
51 sequences at the leaves of each connected sub tree. These groups are
52 each given a different colour, which are reflected in other windows
53 in the same way as if the sequence ids were selected, and can be
54 edited in the same way as user defined sequence groups.
57 Tree partitions are useful for comparing clusters produced by
58 different methods and measures. They are also an effective way of
59 identifying specific patterns of conservation and mutation
60 corresponding to the overall phylogenetic structure, when combined
61 with the <a href="../colourSchemes/conservation.html">conservation
62 based colour scheme</a>.
65 <strong><em>Selecting Subtrees and changing the branch
66 order and subtree group colour</em></strong><br> Moving the mouse over an
67 internal node of the tree will highlight it. You can then :
69 <li>Click the highlighted node to select all the sequences in
71 <li>Double-click the highlighted node to rearrange the tree
72 diagram by inverting the branch ordering at that node.
73 <li>Right-click to open the 'Select Sub-Tree Colour' dialog
74 box, to pick a new colour for the sub-tree and associated
79 <strong><a name="menus"> File Menu</a></strong>
81 <p>This menu allows the displayed tree to be saved as a Newick
82 tree file (Save→Newick File), printed or exported as an image
83 (PNG) or Postscript file. Finally, data used to calculate the tree
84 can be retrieved with the 'Input Data...' entry.</p>
86 <strong>View Menu</strong>
88 <p>When the tree viewer is opened, it displays all the annotation
89 associated with a tree. Trees calculated by Jalview have branch
90 lengths, which correspond to the distance measure used to construct
91 the tree. Tree imported from outside may also contain bootstrap
92 information, and additional leaves from sequences not present in the
93 associated alignment.</p>
94 <p>The view menu mostly contains options controlling the way a
95 tree is rendered and labeled:
97 <li><strong>Fit to Window</strong>
98 <p>The tree layout will be scaled to fit in the display window.
99 You may need to reduce the font size to minimise the leaf label
100 overlap when this option is selected.</p></li>
101 <li><strong>Font Size ...</strong><em>n</em>
103 Brings up a dialog box to set the font size for the leaf names.
104 <em>n</em> is the current font size.
106 <li><strong>Show Distances</strong>
107 <p>Labels each branch or leaf with its associated branch length.</p></li>
108 <li><strong>Show Bootstrap values</strong>
109 <p>Labels each branch or leaf with its associated bootstrap
111 <li><strong>Mark unlinked leaves</strong>
112 <p>Toggles the display of a '*' at the beginning of a leaf label
113 to indicate that there is no sequence corresponding to that leaf
114 in the associated alignment.</p></li>
115 <li><strong>Sort Alignment By Tree</strong>
117 Sorts any associated alignment views using the current tree. (<em>Only
118 available in the Jalview Desktop</em>)
120 <li><strong>Associate Leaves with ...</strong>
122 Only visible when there are <a
123 href="../features/multipleviews.html"
124 >multiple views</a> of the same alignment to show and edit which
125 alignment views are associated with the leaves of the displayed