<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<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>
-<p>
- 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>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.
+ <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>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 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>.
+ </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>
- 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>.</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. 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 contains options controlling the way a tree is
-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>
-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>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>
+ </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>
git://source.jalview.org / jalview.git / blobdiff