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Open Access Methodology article

A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions

Martin Bader1*, Mohamed I Abouelhoda23 and Enno Ohlebusch1

Author Affiliations

1 Institute of Theoretical Computer Science, University of Ulm, 89069 Ulm, Germany

2 Faculty of Engineering, Cairo University, Giza, Egypt

3 Nile University, Giza, Egypt

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BMC Bioinformatics 2008, 9:516  doi:10.1186/1471-2105-9-516

Published: 4 December 2008

Abstract

Background

Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes.

Results

In this paper, we present a new heuristic algorithm that directly constructs a phylogenetic tree w.r.t. the weighted reversal and transposition distance. Experimental results on previously published datasets show that constructing phylogenetic trees in this way results in better trees than constructing the trees w.r.t. the reversal distance, and recalculating the weight of the trees with the weighted reversal and transposition distance. An implementation of the algorithm can be obtained from the authors.

Conclusion

The possibility of creating phylogenetic trees directly w.r.t. the weighted reversal and transposition distance results in biologically more realistic scenarios. Our algorithm can solve today's most challenging biological datasets in a reasonable amount of time.