Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Journal of Computer and System Sciences - Special issue on bioinformatics II
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Parallel construction of conflict graph for phylogenetic network problem
PReMI'07 Proceedings of the 2nd international conference on Pattern recognition and machine intelligence
Parallel algorithm for conflict graph on OTIS-triangular array
ICDCN'08 Proceedings of the 9th international conference on Distributed computing and networking
Accurate computation of likelihoods in the coalescent with recombination via parsimony
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Large neighbourhood search algorithms for the founder sequence reconstruction problem
Computers and Operations Research
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RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Improved recombination lower bounds for haplotype data
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A new recombination lower bound and the minimum perfect phylogenetic forest problem
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
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We consider the following problem: Given a set of binary sequences, determine lower bounds on the minimum number of recombinations required to explain the history of the sample, under the infinite-sites model of mutation. The problem has implications for finding recombination hotspots and for the Ancestral Recombination Graph reconstruction problem [29]. Hudson and Kaplan [15] gave a lower bound based on the four-gamete test. In practice, their bound R_m often greatly underestimates the minimum number of recombinations. The problem was recently revisited by Myers and Griffiths [22], who introduced two new lower bounds R_h and R_s which are provably better, and also yield good bounds in practice. However, the worst-case complexities of their procedures for computing R_h and R_s are exponential and super-exponential, respectively. In this paper, we show that the number of nontrivial connected components, R_c, in the conflict graph [4] for a given set of sequences, computable in time O(nm^2), is also a lower bound on the minimum number of recombination events. We show that in many cases, R_c is a better bound than R_h. The conflict graph was used by Gusfield et al. [4] to obtain a polynomial time algorithm for the galled tree problem, which is a special case of the Ancestral Recombination Graph (ARG) reconstruction problem. Our results also offer some insight into the structural properties of this graph and are of interest for the general Ancestral Recombination Graph reconstruction problem.