Subtree pruning and regrafting (SPR) 

In maximum likelihood Phylogenies, tree optimisation by Subtree pruning and regrafting (SPR) topological rearrangements are usually sufficient to intensively search the tree space. Two new methods are proposed to make SPR moves more efficient. The first method uses a fast distance-based approach to detect the least promising candidate SPRmoves, which are then simply discarded. The second method locally estimates the change in likelihood for any remaining potential SPRs, as opposed to globally evaluating the entire tree for each possible move. These two methods are implemented in a new algorithm with a sophisticated filtering strategy, which efficiently selects potential SPRs and concentrates most of the likelihood computation on the promising moves. (Gascuel 2005)