3 <title>The Tree Viewing Window</title>
6 <p><strong>The Tree Viewing Window</strong></p>
8 The tree viewing window is opened when a tree has been <a href="tree.html">calculated
9 from an alignment</a>, or imported via a file or web service. It includes <a href="#menus">menus</a> for
10 controlling layout and file and figure creation, and enables
11 various selection and colouring operations on the
12 associated sequences in the alignment.</p>
14 <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
15 Selecting sequence ids at the leaves of the tree selects the
16 corresponding sequences in the original alignment. These selections
17 are also reflected in any other analysis windows associated with the
18 alignment, such as another tree viewer.</p>
19 <p><strong><em>Grouping sequences by partitioning the tree at a particular distanec</em></strong><br>
20 Clicking anywhere along the extent of the tree (but not on a leaf or
21 internal node) defines a tree 'partition', by cutting every branch
22 of the tree spanning the depth where the mouse-click occurred. Groups
23 are created containing sequences at the leaves of each connected
24 sub tree. These groups are each given a different colour, which are
25 reflected in other windows in the same way as if the sequence ids
26 were selected, and can be edited in the same way as user defined
29 <p>Tree partitions are useful for comparing clusters produced by
30 different methods and measures. They are also an effective way of
31 identifying specific patterns of conservation and mutation
32 corresponding to the overall phylogenetic structure, when combined
33 with the <a href="../colourSchemes/conservation.html">conservation
34 based colour scheme</a>.</p>
36 <strong><em>Selecting Subtrees and changing the branch order and subtree group colour</em></strong><br>
37 Moving the mouse over an internal node of the tree will highlight
38 it. You can then : <ul>
39 <li>Click the highlighted node to select all the sequences in that branch.
40 <li>Double-click the highlighted node to rearrange the tree
41 diagram by inverting the branch ordering at that
43 <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
44 pick a new colour for the sub-tree and associated sequences.
47 <p><strong><a name="menus">
48 File Menu</a></strong></p>
49 <p>This menu allows the displayed tree to be saved as a Newick tree
50 file (Save→Newick File), printed or exported as an image (PNG) or
51 Postscript file. Finally, data used to calculate the tree can be
52 retrieved with the 'Input Data...' entry.
54 <p><strong>View Menu</strong></p>
55 <p>When the tree viewer is opened, it displays all the annotation
56 associated with a tree. Trees calculated by Jalview have branch
57 lengths, which correspond to the distance measure used to construct
58 the tree. Tree imported from outside may also contain bootstrap information,
59 and additional leaves from sequences not present in the associated
62 <p>The view menu contains options controlling the way a tree is
63 rendered and labelled:
65 <li><strong>Fit to Window</strong><p>
66 The tree layout will be scaled to fit in the display
67 window. You may need to reduce the font size to minimise the leaf
68 label overlap when this option is selected.
70 <li><strong>Font Size ...</strong><em>n</em><p>
71 Brings up a dialog box to set the font size for the leaf
72 names. <em>n</em> is the current font size.
74 <li><strong>Show Distances</strong><p>
75 Labels each branch or leaf with its associated branch
77 <li><strong>Show Bootstrap values</strong><p>
78 Labels each branch or leaf with its associated bootstrap value.
80 <li><strong>Mark unlinked leaves</strong><p>
81 Toggles the display of a '*' at the beginning of a leaf label to
82 indicate that there is no sequence corresponding to that leaf in the
85 <li><strong>Associate Leaves with ...</strong><p>
86 Only visible when there are <a href="../features/multipleviews.html">multiple views</a> of the same
87 alignment to show and edit which alignment views are associated with
88 the leaves of the displayed tree.