When a tree has been calculated from an alignment, or imported via a
file or web service it is displayed by Jalview's tree viewing
window. Trees can be rearranged, used to select sequences and groups
- in the associated alignment, saved in newick format or exported as an
+ in the associated alignment, saved in Newick format or exported as an
image or postscript file.</p>
<p>
Selecting sequence ids at the leaves of the tree selects the
are also reflected in any other analysis windows associated with the
alignment, such as another tree viewer.</p>
-<p>
- Clicking on an internal node of the tree will rearrange the tree
- diagram, inverting the ordering of the branches at that node.
+<p>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>
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 occured. Groups
+ of the tree spanning the depth where the mouse-click occurred. Groups
are created containing sequences at the leaves of each connected
- subtree. These groups are each given a different colour, which are
+ 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 clusterings produced by
+<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
based colour scheme</a>.</p>
<p><strong>File Menu</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.
+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,
-or additional leaves from sequences not present in the associated
-alignment.
+and additional leaves from sequences not present in the associated
+alignment.
</p>
<p>The view menu contains options controlling the way a tree is
-rendered and labelled:</p>
-<p><ul>
+rendered and labelled:
+<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>
+<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>
+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.
+indicate that there is no sequence corresponding to that leaf in the
+associated alignment.
</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>