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  HyPhy Documentation: GUI Components: Viewing Trees

Overview

Tree panel is a tool for displaying, editing, printing and saving trees (phylogenies). It may also be used to edit parameter values for branch models and define new scaling variables to display the tree with. Tree panel can opened in a variety of ways: reading a tree from a file, using parameter tables, using the object inspector (Command-I or select it from the 'Windows Menu'), or using the OpenWindow command of the batch language. By default, if an analysis produces a single tree, that tree is automatically displayed after the analysis is complete.

Viewing Modes

The are two major tree viewing modes:

Scrolling: the viewing area is fixed, and the user scrolls to bring hidden portions of the tree into view. The navigation rectangle in the top left corner shows a miniature version of the tree, and the orange rectangle represents the portion of the tree currently displayed in the main pane.

The first four buttons control the spacing between branches; use them to effect horizontal/vertical expansion or contraction. The fifth button changes the orientation of the tree from left-right to top top-bottom. The sixth button fits the entire tree inside the main viewing pane. The last button controls the parameters of a fish-eye projection view to be discussed later.

Scaling: the tree is forced to always fit to the viewing pane, and resizing the window will resize the tree as well.

The navigation pane is removed and scaling buttons are disabled. To activate the scaling view, select 'Tree Display Options' from the tree menu and check 'Scale tree by resizing the window'.

Tree Styles.
Rectangular: default mode. Well suited for displaying labeled/scaled trees. Straight: Works well only on rooted binary trees.
Smooth Edges. Very similar to the rectangular mode. Radial: Works well for visualizing unrooted trees.

For radial views, the user can adjust the radial angle that the tree should be laid out in. By default the full angle (0 to 2pi, approx 6.284) radian is used. To change the default, set starting and ending angles (in radian) using 'Tree Display Options' dialog. The dialog provides visual feedback for the angle.

Start Angle = 0,
End Angle = 3.14 (pi)
Upper Halfplane
Start Angle = 1.57 (pi/2),
End Angle = 3.14 (pi)
Upper-Right Quarterplane

Labeling

Following are some labelings of the tree produced by the 'HKY85.bf' analysis from the 'SimpleAnalysis' folder of 'Examples'. Run the analysis, then choose the menu 'Analysis', submenu 'Trees', item 'givenTree' to obtain the tree.
Label leaves only (default). Label leaves and internal nodes.
'Internal Labels' from the 'Tree Menu' toggles this option.

The user can select the font to use from the 'Tree Display Options' dialog. Also, the user can choose to label tree branches with numeric values (for more on that, see the section on scaling). The next display uses line width of 3, font Arial (size 12) and labels branches with their lengths (expected number of substitutions per site). The shortest branches aren't labeled, because there isn't enough space to fit the label along that branch. Branch labels are controlled via the 'Branch Labels' submenu of the 'Tree Menu'. Branch length labels only work in rectangular horizontal mode.

Saving and printing.

The user can save the tree as a picture (in a number of formats supported by Quicktime), as a Newick string or a NEXUS tree block. Use the 'Save' command from the 'File' menu to access this functionality.

The trees can also be printed (and saved as PostScript and PDF files, by printing to a file). Presently, all trees are scaled to fit in one page, whose orientation (landscape or portrait) is determined by printing options. The ability to span multiple pages when printing is planned for future releases.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002