Starting with MegAlign Pro version 17.2.1 (coming January 2020), each tree in the Tree view displays an incoming root edge, which is intended to represent the location of a possible common ancestor. The root edge appears on the left of a tree drawn in the default orientation.

For purposes of visualization or publication, you may wish to root the tree or choose a different location for the root. For example, you may wish to balance the tree by moving the root to a long branch.

To reroot a tree, use the Tree > Root On subcommands or press the Sort sequences tool () in the Tree view and use the Root On commands there.

  • Root On > Selected Branch places the root at the base of the currently selected branch. After selecting CP002076 in the example tree above, this command yielded the following tree:

  • Root On > Midpoint Branch computes the midway point between the two leaf nodes that are farthest apart and places the root there. This can result in a more balanced tree. Using this command with the example tree yielded the following tree:

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