A practical algorithm for ancestral rearrangement reconstruction

Authors:
Jakub Kováč;Broňa Brejová;Tomáš Vinař
Affiliations:
Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia;Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia;Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
Venue:
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Year:
2011

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Abstract

Genome rearrangements are a valuable source of information about early evolution, as well as an important factor in speciation processes. Reconstruction of ancestral gene orders on a phylogeny is thus one of the crucial tools contributing to understanding of evolution of genome organization. For most models of evolution, this problem is NP-hard. We have developed a universal method for reconstruction of ancestral gene orders by parsimony (PIVO) using an iterative local optimization procedure. Our method can be applied to different rearrangement models. Combined with a sufficently rich model, such as the double cut and join (DCJ), it can support a mixture of different chromosomal architectures in the same tree. We show that PIVO can outperform previously used steinerization framework and achieves better results on real data than previously published methods. Datasets, reconstructed histories, and the software can be downloaded at http://compbio.fmph.uniba.sk/pivo/