Xml Input File
Assign Branch Lengths
The tree view allows the user to visualize, modify, and print trees and mutational hostories. This window can be opened once an input file has been loaded by selecting Trees->Tree View from the application menu (alternatively, you can use the Cmd-T keyboard shortcut).
The left part of window contains a number of options for changing how the current tree is being displayed, which tree to display, and which characters to be displayed (and parameters, if required) and to be used when a single map for display is being simulated. Briefly from top to bottom these are:
- Zoom: The magnification of the tree image can be adjusted by moving the slider to the left (decrease zoom) and right (increase zoom).
- Colors: The user can change the Default branch color, Taxon labels colors, Background color, and state colors.
- Labels: The user can select to display or not display taxon labels (Show taxon labels) and states (Show states). In addition, the font size can be selected.
- Info: Displays information about the input file.
- Map: This box allows the user to generate a mutational map for the selected character, tree, and parameter combination (for information on configuring the model see here) by clicking the Map button or using the Cmd-M keyboard shortcut. Select the up and down buttons to change the tree, character, or parameter set.