1. Include/Exclude Taxa: The user can opt to include or exclude taxa from the Data View using a pop down window. These actions are cosmetic and have no effect on the analysis. This options is available to allow users to define the taxa to be included when saving the data matrix to a new file in a new format. (For excluding taxa from the analysis they need to be pruned from the tree. See the help documents here for more information.)
2. Include/Exclude Characters: Selecting this options opens an attached window that allows users to exclude or include characters available to the analysis. This option also effects the output when the data matrix is saved to a new file. (For more information on saving a modified data matrix to a new file format see the help documents here).
3. State Colors: Changes which colors are used when displaying the character state in the Data View window and Tree View window. (More information can be found in these places: Tutorial (Lesson 3 ⇒ Changing State Colors) and documents on the Users Preferences.
4. Character Coding: Sets how molecular and morphological characters are interpreted by the evolutionary model. (For more information view the documents here. [Character Coding pages])
5. More File Info: Opens a window dislplaying information about the file; file name, file path, number of sites, number of taxa, and the data type. This window also displays information about the other three files: trees file, histories file, and parameters file.
6. Save Data Matrix: The data matrix can modified and saved to a new file. Options exist for selecting the new file format and output style. (For more information go to the help pages here. [Saving Data Matrix])

1. Display Options: Opens a window that offers different options for changing how different aspects are displayed in the Tree View window, such as branch color. (See the help documents here for detailed information on the options. [Modify Tree Display])
2. Root Tree: Opens a window allowing the user to defined the outgroup taxa and determine how the program interprets outgroup species during an analysis and displays the outgroup species. (For more information see the help documents here. [Rooting Trees])
3. Clear Map: Clears the character history from the display. Branches are shown in the default color as defined by the user (the porgram default is black as shown on the right).
4. More File Info: Opens a window dislplaying information about the file; file name, file path, number of taxa, and the number of trees. This window also displays information about the other three files: trees file, histories file, and parameters file.
5. Modifications: Tree modifications are options that allow the user to manipulate how the tree is displayed and, most importantly, a number of options applied during data analysis. For example, the user can define constraints and fix ancestral states at nodes. This feature in the Tree View window shows whether window will respond to mouse actions over different parts of the tree (Yes, No). To activate mouse driven tree modifications select Turn on Tree Modifications item in the Trees main menu item, or activate it using the L keyboard shortcut. (For more information of modifiying the tree see the help documents here. [Tree Manipulation (Modifications)]) Rooting the tree and changing other display options are set elsewhere in the program.
6. Click here to zoom view: Zooms the image of the tree for closer inspection fo character histories.
7. Map: Generates a character history for the currently selected character. The default character to be mapped is character one (alternatively, use the M keyboard shortcut).

1. Check All: This changes the "checked" state of rows shown in the parameter view by activating them all with a check mark. Unchecked rows can be excluded from use during the analysis.
2. Uncheck All: This changes the "checked" state of rows shown in the parameter view by de-activating them all, removing the check mark. Unchecked rows can be excluded from use during the analysis.
3. Parameter header labels: This displays capitalised versions of the headers as defined in the header column of the parameter file.
4. More File Info: Opens a window dislplaying information about the file; file name, file path, number of parameters, and the number of parameter samples. This window also displays information about the other three files: trees file, histories file, and parameters file.