Faster exact computation of rSPR distance View Full Text


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Article Info

DATE

2013-12-08

AUTHORS

Zhi-Zhong Chen, Ying Fan, Lusheng Wang

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 O2.415dn\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$O\left( 2.415^dn\right) $$\end{document} time, where n\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n$$\end{document} and d\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$d$$\end{document} 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 O2.344dn\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$O\left( 2.344^dn\right) $$\end{document} 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. More... »

PAGES

605-635

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s10878-013-9695-8

DOI

http://dx.doi.org/10.1007/s10878-013-9695-8

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1001021632


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