Abstract
Calculating the rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a frequently applied process in various areas of molecular evolution. However, computing this distance is an NP-hard problem and practical algorithms for computing it exactly are rare. In this paper, a divide-and-conquer approach to calculating the rSPR distance is established. This approach breaks the problem instance into a number of smaller and more tractable subproblems. Two reduction rules which were previously used to show that computing the rSPR distance is fixed-parameter tractable can easily be used to complement this new theoretical result, and so a significant positive impact on the running time of calculating this distance in practice is likely.
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We thank the New Zealand Marsden Fund for their support.
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Linz, S., Semple, C. A Cluster Reduction for Computing the Subtree Distance Between Phylogenies. Ann. Comb. 15, 465–484 (2011). https://doi.org/10.1007/s00026-011-0108-3
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DOI: https://doi.org/10.1007/s00026-011-0108-3