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
31 href="tree.html">calculated from an alignment</a>, or
32 imported via a file or web service. It includes <a href="#menus">menus</a>
33 for controlling layout and file and figure creation, and enables
34 various selection and colouring operations on the associated
35 sequences in the alignment.
38 <strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
39 Selecting sequence IDs at the leaves of the tree selects the
40 corresponding sequences in the original alignment. These selections
41 are also reflected in any other analysis windows associated with the
42 alignment, such as another tree viewer.
45 <strong><em><a name="partitioning">Grouping
46 sequences by partitioning</a> the tree at a particular distance</em></strong><br>
47 Clicking anywhere along the extent of the tree (but not on a leaf or
48 internal node) defines a tree 'partition', by cutting every branch of
49 the tree spanning the depth where the mouse-click occurred. A red line
50 will be shown where the partition was made, and groups are created
51 containing sequences at the leaves of each connected sub tree. These
52 groups are each given a different colour, which are reflected in other
53 windows in the same way as if the sequence IDs were selected, and can
54 be 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>.To distinguish parts of the alignment assigned
63 to different groups, you may also enable the Sequence ID colour
64 scheme via the <a href="../menus/alwcolour.html">Alignment
65 window's Colours menu</a> (<em>Since 2.11</em>).
68 <strong><em>Selecting Subtrees and changing the branch
69 order and subtree group colour</em></strong><br> Moving the mouse over an
70 internal node of the tree will highlight it. You can then :
72 <li>Click the highlighted node to select all the sequences in
74 <li>Double-click the highlighted node to rearrange the tree
75 diagram by inverting the branch ordering at that node.
76 <li>Right-click to open the 'Select Sub-Tree Colour' dialog
77 box, to pick a new colour for the sub-tree and associated
82 <strong><a name="menus"> File Menu</a></strong>
84 <p>This menu allows the displayed tree to be saved as a Newick
85 tree file (Save→Newick File), printed or exported as an image
86 (PNG) or Postscript file. Finally, data used to calculate the tree
87 can be retrieved with the 'Input Data...' entry.</p>
89 <strong>View Menu</strong>
91 <p>When the tree viewer is opened, it displays all the annotation
92 associated with a tree. Trees calculated by Jalview have branch
93 lengths, which correspond to the distance measure used to construct
94 the tree. Tree imported from outside may also contain bootstrap
95 information, and additional leaves from sequences not present in the
96 associated alignment.</p>
97 <p>The view menu mostly contains options controlling the way a
98 tree is rendered and labeled:
100 <li><strong>Fit to Window</strong>
101 <p>The tree layout will be scaled to fit in the display
102 window. You may need to reduce the font size to minimise the
103 leaf label overlap when this option is selected.</p></li>
104 <li><strong>Font Size ...</strong><em>n</em>
106 Brings up a dialog box to set the font size for the leaf names.
107 <em>n</em> is the current font size.
109 <li><strong>Show Distances</strong>
110 <p>Labels each branch or leaf with its associated branch
112 <li><strong>Show Bootstrap values</strong>
113 <p>Labels each branch or leaf with its associated bootstrap
115 <li><strong>Mark unlinked leaves</strong>
116 <p>Toggles the display of a '*' at the beginning of a leaf
117 label to indicate that there is no sequence corresponding to
118 that leaf in the associated alignment.</p></li>
119 <li><strong>Sort Alignment By Tree</strong>
121 Sorts any associated alignment views using the current tree. (<em>Only
122 available in the Jalview Desktop</em>)
124 <li><strong>Associate Leaves with ...</strong>
126 Only visible when there are <a
127 href="../features/multipleViews.html">multiple
128 views</a> of the same alignment to show and edit which alignment
129 views are associated with the leaves of the displayed tree.