Resolve mode is only applicable to non-binary gene trees. Its function is to resolve polytomies in a non-binary gene tree by comparing it with a binary species tree, resulting in one or more binary tree(s) with minimal D/L Score.
Specifically, the Resolve function removes all polytomies in the original gene tree, and uses an algorithm similar to the rearrangement algorithm to replace them with new edges such that: 1) the new tree is binary, and 2) the new tree has optimal D/L Score. Note that each edge in the original non-binary gene tree still exists in the resulting binary gene tree.
There may be more than one binary tree that agrees with the input tree at all edges except polytomies and has minimal D/L Score. In this case, the user can investigate these optimal alternate hypotheses using a point and click interface as in Rearrange mode. See Section 7.1 - Alternate Optimal Hypotheses for a more detailed explanation of alternate hypotheses.
Selecting the “Highlight Polytomies” checkbox will highlight in cyan all vertical edges representing polytomies in the tree, allowing the user to see which nodes will be resolved. After running the resolve algorithm, the “Highlight New Edges” checkbox will be selected, and will highlight in cyan all those edges in the gene tree that were previously represented by the polytomy (see Figure 8.1). This option is only available in Resolve mode.
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Figure 8.1: (a) Polytomies in the gene tree can be highlighted in cyan while in the Resolve task mode. (b) After the polytomies are resolved, edges that were not present in the original tree are highlighted in cyan.
To resolve the gene tree:
A minimum cost binary resolution of all polytomies in the tree will appear in the tree panel. Note that the new edges will not have edge weights.
If the gene tree is binary, the “Resolve Polytomies” button will be grayed out.
NOTE: If asked to resolve a tree that has not been reconciled, Notung will first invoke the reconciliation algorithm. In this case, the user is asked to select a species tree for reconciliation.
To highlight all polytomies (default: OFF):
All vertical edges representing polytomies in the tree will be highlighted.
To highlight all new edges (default: ON, after resolving):
All edges that were represented by the polytomies in the original tree will be highlighted.
To view alternate optimal event histories:
The tree panel will now show a new tree corresponding to the selected alternate history.
If there is only one optimal history or if the polytomies have not been resolved, the drop down menu will be grayed out.
To swap individual nodes:
NOTE: If there are no swappable nodes in the tree or if the polytomies have not been resolved, this button will be grayed out.Swappable nodes are marked with an enlarged blue and cyan square. As you pass the mouse over a swappable node, other nodes that can be interchanged with it with are temporarily highlighted with a light orange triangle. Swappable nodes that are not currently visible in the tree panel (for instance, if you have zoomed in), are indicated by arrows in the tree panel pointing in the direction of those nodes.
The node you selected is highlighted with a blue triangle. Nodes with which it can be swapped are now highlighted with pink triangles.
NOTE: When a different alternate event history is selected in the “Select an optimal event history” list, Notung rebuilds the tree from data saved at the time of resolution. Any manual swaps made to a previously viewed event history will be lost. Therefore, if you wish to save information after a manual swap, you must save your tree. See Chapter 3.3 - Opening and Saving Trees for more information.