The Tree Viewer display can be controlled using the toolbar buttons. More advanced settings can be made by using the Tree Viewer Options dialog box.
TO SET the display options for the Tree Viewer window
1. Select the preferences button in the tree viewer window.
The Tree Viewer Options dialog box is displayed.
2. To adjust the appearance of the sequence name labels, use the font, size, and style drop-down menus in the Name Labels panel.
3. To adjust the appearance of the branch labels, use the controls in the Name Labels panel:
- The Visible check box controls whether or not the labels are displayed. By default the check box is selected and the labels are displayed
- To change the appearance of the branch labels, use the font, size, and style drop-down menus.
4. When a bootstrap tree is being displayed, you can use the controls in the Bootstrap Filter panel to control the display threshold values:
- Use the Collapse nodes < text box to set the threshold percentage occurrence for a node to be displayed in the bootstrap tree. Nodes occurring less frequently than this value will be collapsed. You may enter any value from 50 through 100. The default is 50%.
- Use the Label nodes > text box to set the threshold for labeling a node's percentage occurrence in the bootstrap tree. Nodes occurring less frequently than this value will not be labeled. You may enter any value from 50 through 100, provided it is not less than the Collapse nodes value. The default is 70%.
The Bootstrap Filter controls are disabled when there is no bootstrap tree in the window.
5. To change the rooting of a tree generated using the neighbor joining method, select the appropriate Rooting radio button:
- Unrooted : the tree will not be rooted. This is the default setting for neighbor joining trees
- Midpoint rooting: the tree will be rooted on its center of gravity
- Outgroup rooting: the tree will be rooted on its longest branch.
If you have already rooted the tree manually using the rooting button, selecting this radio button has no effect.
Rooting controls are disabled if the current tree was calculated using UGPMA, because that method always roots the tree.
6. To adjust the rule for displaying any branches with calculated lengths that are negative, do one of the following in the Negative branch lengths panel:
- Select Collapse to zero if you want to collapse such branches in the display. This is the default setting
- Select Mark as dashed line to indicate negative lengths by dashed lines.
Negative branch lengths controls are available only when a phylogram display has been selected.
7. To display details of the methods used to calculate the phylogeny, select the Display summary of parameters check box.
8. Select OK to apply the settings and close the dialog box.
Alternatively, select Defaults to restore the program default settings, or Cancel to close the dialog box without applying or saving any changes.