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Bioinformatics 2008 24(13):i132-i138; doi:10.1093/bioinformatics/btn150
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The multiple gene duplication problem revisited

Mukul S. Bansal and Oliver Eulenstein *

Department of Computer Science, Iowa State University, Ames, IA 50011, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known.

Results: In this article we solve this longstanding open problem by providing the first exact and efficient solution. We also demonstrate the improvement offered by our algorithm over the best heuristic approaches, by applying it to several simulated as well as empirical datasets.

Contact: oeulenst{at}cs.iastate.edu


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