3.5. SPECTRE Viewer¶
The SPECTRE Viewing tool allows users to visualise trees and networks stored in a nexus file. An example screenshot of a loaded networking is shown below. The window is broken up from top to bottom into the menu bar, viewing canvas and status bar.
The viewer allows the user to navigate the network through pan, zoom and rotate controls. Additionally, properties of nodes can be altered, such as label positions, size and styles.
We will describe the functions the viewer offers by describing the menu bar items.
3.5.4. Labelling Options¶
The viewer provides multiple options for controlling the look, feel and positioning of labelled nodes in the network. These options are controlled via the Labelling menu.
Show labels - Turns on or off whether node labels should be visible (Ctrl-L)
Color labels - Turns on or off whether the labels color should be inverted (i.e. Black text on white background, or white text in a black box). This option is only relevant if show labels is switched on.
Format selected nodes - Clicking on this option brings up a dialog box that allows users to modify the shape, size and color of the currently selected nodes. In addition, they can modify the size and style of the current selected nodes’ label text.
Fix all label positions - This forces the labels to stay in the same proximity to the node as current viewed, even after the image is rotated or flipped.
Leaders - Sometimes taxa labels would be placed so close to each other that the text would overlap on the screen. This often occurs with internal nodes. To avoid this problem labels towards the edge of the window and joined to the network node via a “leader” line in order to aid readability. This sub-menu allows the user to control the look and feel of the leaders.
3.5.5. Tools¶
The SPECTRE graphical interface can also launch other tools in the package. These are launched via the Tools menu and will create a separate window where the user can specify input and output files as well as parameters to be passed to the algorithms. Details regarding the graphical interface for each tool are described along with the associated documentation.