Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Summarizing Multiple Gene Trees Using Cluster Networks
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Improved Layout of Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Drawing Rooted Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Reconstructing phylogenetic networks with one recombination
WEA'08 Proceedings of the 7th international conference on Experimental algorithms
Reducing distortion in phylogenetic networks
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
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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@informatik.uni-tuebingen.de