Figure 27.12. Subtree pruning and regrafting. In this alternating tree-generating method, a subtree on a larger tree is selected, such as the circled subtree in A. This subtree is then removed (“pruned”) from the tree and reattached (“regrafted”) at a different position. For tree searching, the process is repeated for all possible regrafting locations (arrows) and the tree with the best score is selected for further analysis. (Redrawn from http://www.scs.fsu.edu/~ronquist/compgen/LectPhyloI.pdf.)

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