Walks on SPR Neighborhoods

@article{Caceres2011WalksOS,
  title={Walks on SPR Neighborhoods},
  author={Alan Joseph J. Caceres and Juan Castillo and Jinnie Lee and Katherine St. John},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2011},
  volume={10},
  pages={236-239}
}
A nearest-neighbor-interchange (NNI)-walk is a sequence of unrooted phylogenetic trees, T1,T2, ... ,Tk where each consecutive pair of trees differs by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that visit all trees in a subtree-prune-and-regraft (SPR) neighborhood of a given tree. For any unrooted, binary tree, T, on n leaves, the shortest walk takes ⊖(n2) additional steps more than the number of trees in the SPR neighborhood. This answers Bryant's Second… 
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Characterizing Local Optima for Maximum Parsimony

It is shown that when neighbors are defined via the subtree prune and regraft metric, there is a single local optimum for perfect sequence data, and thus, every such search finds a global optimum quickly.

Characterizing Local Optima for Maximum Parsimony

It is shown that when neighbors are defined via the subtree prune and regraft metric, there is a single local optimum for perfect sequence data, and thus, every such search finds a global optimum quickly.

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