The Tree Viewer window can be used to display:
- phylogenetic trees
- guide trees used to generate ClustalW multiple alignments.
It includes tools for rooting trees to emphasize the direction of evolution, deleting parts of the tree, rotating nodes to re-order the sequences, and formatting the tree diagram for publication.
The shaded header area of the Tree Viewer window contains a row of buttons that are used to perform special functions. Note that the leftmost icon (tree) is not an action button, but serves to identify the Tree Viewer window. The other icons are as follows:
- Tree shape selection. This button (second from the left) lets you select the type of tree displayed: slanted cladogram, rectangular cladogram, or phylogram.
- Rooting. Use this button to select an outgroup.
- Rotate. Use this button to change the order in which two nodes are arranged on the screen.
- Tree focus. Use this button to display only the part of the tree you have selected. To return to a view of the whole tree, double-click anywhere in the window.
- Delete Node. Use this button to delete a part of the tree you have selected.
- Recalculate tree. Use this button to display the Phylogenetic Reconstruction dialog box.
- Font Increase/Decrease. Use this button to adjust the font size in the Tree Viewer window. Each click increases or decreases the font by one increment.
- Line Width. Use this button to adjust the weight of lines in the Tree Viewer display; choose the required line thickness from the drop-down menu.
- Preferences. Click on this button to display the Tree Viewer Preferences dialog box.
At the bottom of the Tree Viewer window are controls for magnification and page mode:
- Page mode. Use this button to either show or hide dotted lines marking the page boundaries for printed output.
- View scale. These controls let you set a magnification for viewing the tree, either by choosing from a drop-down menu or by typing in a text box. The current viewing magnification is displayed.
TIP: The width of a tree display is set to fit the current paper size. If you want to make a tree wider, use File | Page Setup to select a larger paper size or a landscape orientation.