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<html>
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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. A red line
will be shown where the partition was made, and 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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