The state of a gene tree changes each time a Notung operation, such as rooting, rearrangement, reconciliation, or resolution, is performed on the tree. Notung maintains a history of state changes for each gene tree. This history can be accessed via the History panel, allowing the user to return to and operate on a previous state, or visually compare the state before and after a task is performed.
Notung lists the states in the history panel by task name (see Figure 9.1). The first entry in the list is always Start, which is the state of the tree when loaded; others entries may include Changed Parameter Values, Reconciled, Rooting Analysis, Rooting on X, Notung Rearrange, Notung Resolve Polytomies, Select Alternate Optimal History, and Swapped Y and Z, where X is an edge and Y and Z are swapped nodes. The list proceeds from top to bottom in the order tasks were performed, and includes the D/L Score for each state.
NOTE: Previous states in the History panel are not saved in a file. When the gene tree file is closed, the history associated with the current tree is lost. To save trees associated with intermediate states, select the state and click “File → Save As.”
NOTE: Parameter values are saved with each state in the history. For each state in the history, the parameters will correspond to those values used at the time the operation was performed. Any subsequent changes to parameter values will not be applied retroactively.
To view previous states of the gene tree:
Click on image to see larger version
Figure 9.1: The history of a gene tree that had been reconciled, rooted, and rearranged. Currently, the state of the tree after reconciliation and prior to rooting is selected and displayed in the panel.