Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Journal of Computer and System Sciences - Special issue on bioinformatics II
The Fine Structure of Galls in Phylogenetic Networks
INFORMS Journal on Computing
A fundamental decomposition theory for phylogenetic networks and incompatible characters
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
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
Inferring Pedigree Graphs from Genetic Distances
IEICE - Transactions on Information and Systems
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
On the Elusiveness of Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient and practical algorithms for deducing the history of recombination in populations
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
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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Phylogenetic networks are models of sequence evolution that go beyond trees, allowing biological operations that are not tree-like. One of the most important biological operations is recombination between two sequences. An established problem [J. Hein, Reconstructing evolution of sequences subject to recombination using parsimony, Math. Biosci. 98 (1990) 185-200; J. Hein, A heuristic method to reconstruct the history of sequences subject to recombination, J. Molecular Evoluation 36 (1993) 396-405; Y. Song, J. Hein, Parsimonious reconstruction of sequence evolution and haplotype blocks: finding the minimum number of recombination events, in: Proceedings of 2003 Workshop on Algorithms in Bioinformatics, Berlin, Germany, 2003, Lecture Notes in Computer Science, Springer, Berlin; Y. Song, J. Hein, On the minimum number of recombination events in the evolutionary history of DNA sequences, J. Math. Biol. 48 (2003) 160-186; L. Wang, K. Zhang, L. Zhang, Perfect phylogenetic networks with recombination, J. Comput. Biol. 8 (2001) 69-78; S.R. Myers, R.C. Griffiths, Bounds on the minimum number of recombination events in a sample history, Genetics 163 (2003) 375-394; V. Bafna, V. Bansal, Improved recombination lower bounds for haplotype data, in: Proceedings of RECOMB, 2005; Y. Song, Y. Wu, D. Gusfield, Efficient computation of close lower and upper bounds on the minimum number of needed recombinations in the evolution of biological sequences, Bioinformatics 21 (2005) i413-i422. Bioinformatics (Suppl. 1), Proceedings of ISMB, 2005, D. Gusfield, S. Eddhu, C. Langley, Optimal, efficient reconstruction of phylogenetic networks with constrained recombination, J. Bioinform. Comput. Biol. 2(1) (2004) 173-213; D. Gusfield, Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination, J. Comput. Systems Sci. 70 (2005) 381-398] is to find a phylogenetic network that derives an input set of sequences, minimizing the number of recombinations used. No efficient, general algorithm is known for this problem. Several papers consider the problem of computing a lower bound on the number of recombinations needed. In this paper we establish a new, efficiently computed lower bound. This result is useful in methods to estimate the number of needed recombinations, and also to prove the optimality of algorithms for constructing phylogenetic networks under certain conditions [D. Gusfield, S. Eddhu, C. Langley, Optimal, efficient reconstruction of phylogenetic networks with constrained recombination, J. Bioinform. Comput. Biol. 2(1) (2004) 173-213; D. Gusfield, Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination, J. Comput. Systems Sci. 70 (2005) 381-398; D. Gusfield, Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination, Technical Report, Department of Computer Science, University of California, Davis, CA, 2004]. The lower bound is based on a structural, combinatorial insight, using only the site conflicts and incompatibilities, and hence it is fundamental and applicable to many biological phenomena other than recombination, for example, when gene conversions or recurrent or back mutations or cross-species hybridizations cause the phylogenetic history to deviate from a tree structure. In addition to establishing the bound, we examine its use in more complex lower bound methods, and compare the bounds obtained to those obtained by other established lower bound methods.