Heuristics for the inversion median problem

Background: The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three genomes find a fourth that minimizes the sum of the evolutionary distances between itself and the given three. Many exact algorithms and heuristics have been developed for the inversion median problem, of which the best known is MGR. Results: We present a unifying framework for median heuristics, which enables us to clarify existing strategies and to place them in a partial ordering. Analysis of this framework leads to a new insight: the best strategies continue to refer to the input data rather than reducing the problem to smaller instances. Using this insight, we develop a new heuristic for inversion medians that uses input data to the end of its computation and leverages our previous work with DCJ medians. Finally, we present the results of extensive experimentation showing that our new heuristic outperforms a...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret
• Keywords: BMCBI 2010, Genomes, Heuristic, Inversion Medians