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Faster exact computation of rSPR distance

Author

Listed:
  • Zhi-Zhong Chen

    (Tokyo Denki University)

  • Ying Fan

    (City University of Hong Kong)

  • Lusheng Wang

    (City University of Hong Kong)

Abstract

Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees. The rooted subtree prune and regraft (rSPR) distance of the two trees has been used for this purpose, and many algorithms and software tools have been developed for computing the rSPR distance of two given phylogenetic trees. The previously fastest exact algorithm for this problem runs in $$O\left( 2.415^dn\right) $$ O 2 . 415 d n time, where $$n$$ n and $$d$$ d are the number of leaves and the rSPR distance of the input trees, respectively. In this paper, we present a faster exact algorithm which runs in $$O\left( 2.344^dn\right) $$ O 2 . 344 d n time. Our experiments show that the new algorithm is significantly faster than the newest version (namely, v1.1.1) of the previously best software (namely, rSPR) for RSPR distance.

Suggested Citation

  • Zhi-Zhong Chen & Ying Fan & Lusheng Wang, 2015. "Faster exact computation of rSPR distance," Journal of Combinatorial Optimization, Springer, vol. 29(3), pages 605-635, April.
    • Handle: RePEc:spr:jcomop:v:29:y:2015:i:3:d:10.1007_s10878-013-9695-8
    DOI: 10.1007/s10878-013-9695-8
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    References listed on IDEAS

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    1. Bin Ma & Louxin Zhang, 2011. "Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction," Journal of Combinatorial Optimization, Springer, vol. 21(4), pages 409-422, May.
    2. Bin Ma & Lusheng Wang & Louxin Zhang, 1999. "Fitting Distances by Tree Metrics with Increment Error," Journal of Combinatorial Optimization, Springer, vol. 3(2), pages 213-225, July.
    3. Leszek Gasieniec & Jesper Jansson & Andrzej Lingas & Anna Östlin, 1999. "On the Complexity of Constructing Evolutionary Trees," Journal of Combinatorial Optimization, Springer, vol. 3(2), pages 183-197, July.
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    Cited by:

    1. Damir Hasić & Eric Tannier, 2019. "Gene tree reconciliation including transfers with replacement is NP-hard and FPT," Journal of Combinatorial Optimization, Springer, vol. 38(2), pages 502-544, August.

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