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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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- * Jalview is free software: you can redistribute it and/or
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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><a name="partitioning">Grouping sequences by partitioning</a> the
- tree at a particular distance</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>.To distinguish parts of the alignment assigned
- to different groups, you may also enable the Sequence ID colour
- scheme via the <a href="../menus/alwcolour.html">Alignment
- window's Colours menu</a> (<em>Since 2.11</em>).
- </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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