<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>The Tree Viewing Window</title>
</head>
<body>
<p><strong>The Tree Viewing Window</strong></p>
<p>
- 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
- image or postscript file.</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>
- Clicking on an internal node of the tree will rearrange the tree
- diagram, inverting the ordering of the branches at that node.
-</p>
-<p>
+<p><strong><em>Grouping sequences by partitioning the tree at a particular distanec</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
corresponding to the overall phylogenetic structure, when combined
with the <a href="../colourSchemes/conservation.html">conservation
based colour scheme</a>.</p>
-<p><strong>File Menu</strong></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
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
+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>
+<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>
+<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>
-</ul>
+ <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>
git://source.jalview.org / jalview.git / blobdiff