Chapter 6 Rooting Mode

In Rooting mode, the D/L Score can be used to infer the root of a gene tree. Notung’s Rooting Analysis calculates a root score for each edge in the tree, corresponding to the D/L Score of the tree if rooted on that edge. Note that the Rooting Analysis computes root scores, but does not change the tree. The user must root the tree explicitly by clicking in the tree panel. Rooting mode can also be used to root a tree manually by clicking on any edge at any time, even if the Rooting Analysis has not been performed.

When the Rooting Analysis is complete, edges with the minimum root score are highlighted in red. Notung also highlights edges with near optimal scores in pink. Edges with scores that are greater than the minimum by at most 5 percent of the difference between the maximum and minimum score are highlighted in pink. Figure 6.1(a) shows the gene tree from Figure 5.1 after the Rooting Analysis has been applied. Note that optimal rooting edges are highlighted in red, but the gene tree topology is unchanged from Figure 5.1. Figure 6.1(b) shows the tree after it has been rooted by clicking in the tree panel.

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Figure 6.1: (a) The gene tree from Figure 5.1 after completing the Rooting Analysis. (b) The rerooted tree, after the user has clicked on an edge to designate the root.

When the species tree is non-binary, applying Notung’s Rooting analysis to an unrooted, binary gene tree labels the original gene tree with a root score on each edge. This score is a weighted sum of the number of required duplications, conditional duplications, and losses. By default, the cost of conditional duplications is set to zero. Conditional duplications will only influence the root score if this cost is explicitly set to a positive number by the user. For more information on setting parameters, see Chapter 3.5 - Parameter Values.

Rooting analysis when the gene tree is non-binary differs from the binary case in that root scores are assigned to polytomies, as well as edges. Edges and polytomies in the original tree are assigned the D/L Score associated with rooting on that edge or polytomy. If rooting on a polytomy in a non-binary gene tree produces the minimum or near-minimum score, that node will be circled and the vertical edge representing that polytomy will be highlighted in the appropriate color (Figure 6.2).

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Figure 6.2: Rooting analysis for a non-binary gene tree. The optimal root locations are colored in red. If an edge represented by the polytomy can be selected as an optimal root, the polytomy will be circled and colored in red.

To reroot the tree, click on any edge or polytomy in the tree panel. You may root the tree on any edge, not just the highlighted edges. Notung will root the tree on that edge (or polytomy), and recalculate the reconciliation. The D/L Score of the new, rooted tree is displayed in the bottom-left corner of the screen.

Please note that it is not possible to represent an unrooted tree in standard Newick format. Some tree reconstruction programs, therefore, represent an unrooted tree as a rooted tree with a trifurcation (a polytomy with three children) at the root. Notung cannot distinguish between an unrooted, binary gene tree and a rooted gene tree that has a single trifurcation. If such a gene tree is opened and reconciled in Notung, a notification will appear to inform the user that this tree may, in fact, be an unrooted, binary gene tree. Notung will assume that the tree is rooted and non-binary, and will draw the tree and issue diagnostic messages, accordingly. If you consider the tree to be unrooted and binary, you may find this behavior unexpected. If you want Notung to treat the tree as a binary tree, the trifurcation can be removed by rooting the tree in the Rooting panel. The tree can be made binary by manually rooting the tree on any edge; otherwise, the Rooting Analysis may be used to select the edge with the optimal D/L Score.

NOTE: If the tree has not been reconciled before running a Rooting Analysis, Notung will reconcile it automatically. You will be asked to select a species tree for reconciliation (see Chapter 5 - Reconciliation Mode).

To find optimal root edges:

Click the Rooting tab to enter Rooting mode.
Click “Run Rooting Analysis.”

Good roots will be highlighted. If highlighted edges are small, they are circled in the appropriate color to help the user locate them visually. Use the Zoom feature (see Chapter 11.2 - Zoom) to zoom in on these edges.

To show/hide Rooting Analysis results:

In Rooting Mode, the task panel contains several check boxes that allow the user to specify what rooting related information should be displayed.

Click the appropriate checkbox in the Rooting task panel.
√ Highlight good roots (default: ON)
When the “Highlight good roots” box is checked, the low-scoring root edges in the tree are colored (red for the minimum score, pink for scores within 5 percent of the minimum). To remove the highlighting, uncheck the box.
√ Highlight polytomies (default: OFF)
When the “Highlight polytomies” box is checked, vertical edges representing polytomies in the gene tree, if any exist, are highlighted and circled in cyan.
√ Circle small edges (default: ON)
When the “Circle small edges” box is checked, appropriately colored circles appear around small, low-scoring root edges in the tree, if any exist, making it easier to locate them in large trees. To remove the circles, uncheck the box.
√ Display root score (default: OFF)
When the “Display root score” box is checked, the associated D/L Score appears next to each edge and polytomy in the tree. Rooting scores are shown in pink to distinguish them from edge weights, which are displayed in green.

To reroot the tree:

Click on any edge or polytomy of the tree in the tree panel.