2012/05/15 by Mikael Gast, Gast, Mikael, Mathias Hauptmann +1
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #Data Structures and Algorithms (cs.DS) #Distributed #FOS: Biological sciences #FOS: Computer and information sciences #Genome Rearrangement Algorithms #Genomics and Phylogenetic Studies #Parallel #Populations and Evolution (q-bio.PE) #and Cluster Computing (cs.DC) #cs.DC #cs.DS #q-bio.PE
paper · pdf · doi:10.48550/arxiv.1205.3402
17 pages, 10 figures
arxiv created 2012/05/15 · openalex publication_date 2012/05/15 · arxiv updated 2012/05/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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) ⋅ 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.