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Bioinformatics 2005 21(Suppl 2):ii159-ii165; doi:10.1093/bioinformatics/bti1126
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Computing recombination networks from binary sequences

Daniel H. Huson * and Tobias H. Kloepper

Center for Bioinformatics, Tübingen University Sand 14, 72076 Tübingen, Germany

*To whom correspondence should be addressed.

Motivation: Phylogenetic networks are becoming an important tool in molecular evolution, as the evolutionary role of reticulate events, such as hybridization, horizontal gene transfer and recombination, is becoming more evident, and as the available data is dramatically increasing in quantity and quality.

Results: This paper addresses the problem of computing a most parsimonious recombination network for an alignment of binary sequences that are assumed to have arisen under the ‘infinite sites’ model of evolution with recombinations. Using the concept of a splits network as the underlying datastructure, this paper shows how a recent method designed for the computation of hybridization networks can be extended to also compute recombination networks. A robust implementation of the approach is provided and is illustrated using a number of real biological datasets.

Availability: Our implementation of this approach is freely available as part of the SplitsTree4 software, downloadable from www.splitstree.org

Contact: huson{at}informatik.uni-tuebingen.de


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