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arXiv 1205.3402cs.DScs.DCq-bio.PE
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最近邻交换距离的高效并行计算

Efficient Parallel Computation of Nearest Neighbor Interchange Distances

Mikael Gast, Mathias Hauptmann

摘要:

nni-距离是一个著名的系统发育树的距离度量。我们构造了一个有效的并行近似算法的nni-距离的CRCW-PRAM模型运行在O(log n)的时间在O(n)的处理器上。给定两个系统发生树T1和T2,在同一个分类单元上,具有相同的多组边权值,该算法构造一个权值至多为O(log n)\cdot opt的nni-操作序列,其中opt表示将T1变换为T2的nni-操作序列的最小权值.该算法基于DasGupta等人(2000)给出的nni-距离的顺序近似算法。此外,我们发现,确定所谓的好边对之间的两个加权的双的问题可以计算在O(log n)的时间在O(n log n)的处理器。

英文摘要:

The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two phylogenetic trees T1 and T2 on the same set of taxa and with the same multi-set of edge-weights, the algorithm constructs a sequence of nni-operations of weight at most O(log n) \cdot opt, where opt denotes the minimum weight of a sequence of nni-operations transforming T1 into T2 . This algorithm is based on the sequential approximation algorithm for the nni-distance given by DasGupta et al. (2000). Furthermore, we show that the problem of identifying so called good edge-pairs between two weighted phylogenies can be computed in O(log n) time on O(n log n) processors.

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