Notung offers the user a broad range of options for controlling the appearance of the tree panel and the types of information that can be displayed. Visual presentation of trees in Notung can be changed in two ways. One set of options is found in the Display Options, Zoom, and Font menus in the upper left hand corner of the Notung window. These options, which are described in this section, are relevant in all task modes.
In addition, certain visual features can be controlled from individual Task Panels. These features are typically specific to that task and, in most cases, are only visible when the relevant Task Panel is selected. These options, such as highlighting swappable nodes or weak edges and displaying root scores, are described in the relevant mode sections.
Notung allows users to show or hide node and edge labels using the Display Options menu. Checkboxes next to each item in the menu show which display options are turned on. These options are tree specific - changing them in the currently selected tree will not change them in other open trees. To turn on/off a display option:
NOTE: If internal nodes are not labeled in the input gene tree file, Notung assigns internal node names using a counting system. Node names derived this way begin with n or r, followed by number signifying the order in which the node was counted (e.g., n136 or r122). Node names beginning with an r indicate that the node did not exist in the original tree; rather, they were added during rearrangement of weak edges or resolution of a polytomy. These node names may change if other tasks are performed after the rearrangement or resolve task that produced the new internal node(s). Counting may be different for each session, so node names may vary from session to session, depending on how many trees have been opened in Notung.
When reconciling a gene tree with a non-binary species tree, if orthologous genes are absent in two or more children of a polytomy in the species tree, a single loss in an ancestral species is inferred (called a polytomy loss). When this option is turned on, polytomy losses are displayed with the names of species in which the gene is absent, as well as name of the polytomy (see Figure 5.2a). When turned off, combined losses are labeled with the number of species in which the gene is absent, and the name and the size of the polytomy (Figure 5.2b.)
Notung allows users to zoom in on the tree using either the Zoom menu or keypad controls. Users can zoom in on the whole tree, maintaining the tree’s aspect ratio, or on the X or Y axis independently, elongating the vertical or horizontal edges, respectively. These changes apply only to the currently selected tree.
To zoom in on the whole tree:
NOTE: Ctrl/Cmd means to use the “Control” key for Windows or Linux, and the “Command” (open apple) key for Mac OS X. For operations which do not involve clicking on the tree, the “Control” key is used for all three platforms.
To zoom out on the whole tree:
To zoom in on the X axis:
To zoom out on the X axis
To zoom in on the Y axis:
To zoom out on the Y axis:
To fit the whole tree in the tree panel:
Users can modify the font size of tree labels using the Fonts menu or keypad controls. Fonts can be set to one of four sizes or changed incrementally.
To set a font size:
To increase font size incrementally:
To decrease font size incrementally:
NOTE: Selecting “Large fonts” does not display the largest possible font; the font can be made even larger by using the “Increase font size” option.