Finding an Optimal Inversion Median: Experimental Results

Siepel, Adam, Moret, Bernard (2001) Finding an Optimal Inversion Median: Experimental Results. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2149 . Springer Berlin Heidelberg, pp. 189-203. ISBN 978-3-540-42516-8

URL: http://link.springer.com/chapter/10.1007/3-540-446...
DOI: 10.1007/3-540-44696-6_15

Abstract

We derive a branch-and-bound algorithm to find an optimal inversion median of three signed permutations. The algorithm prunes to manageable size an extremely large search tree using simple geometric properties of the problem and a newly available linear-time routine for inversion distance. Our experiments on simulated data sets indicate that the algorithm finds optimal medians in reasonable time for genomes of medium size when distances are not too large, as commonly occurs in phylogeny reconstruction. In addition, we have compared inversion and breakpoint medians, and found that inversion medians generally score significantly better and tend to be far more unique, which should make them valuable in median-based tree-building algorithms.

Item Type: Book Section
Subjects: bioinformatics
bioinformatics > computational biology
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 15 Jan 2015 20:24
Last Modified: 15 Jan 2015 20:24
URI: http://repository.cshl.edu/id/eprint/31039

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