Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
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)
The Fine Structure of Galls in Phylogenetic Networks
INFORMS Journal on Computing
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
Haplotype Inferring Via Galled-Tree Networks Is NP-Complete
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Information Processing Letters
Discrete Applied Mathematics
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Algorithm for haplotype inferring via galled-tree networks with simple galls
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
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)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On a conjecture about compatibility of multi-states characters
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
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
ICDCIT'05 Proceedings of the Second international conference on Distributed Computing and Internet Technology
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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Phylogenetic networks are models of sequence evolution that go beyond trees, allowing biological operations that are not consistent with tree-like evolution. One of the most important of these biological operations is (single-crossover) recombination between two sequences. An established problem (Math. Biosci. 98 (1990) 185; J. Mol. Evol. 36 (1993) 396; Proceedings of the 2003 Workshop on Algorithms in Bioinformatics, Berlin, Germany, Lecture Notes in Computer Science, Springer, Berlin, 2003; J. Math. Biol. 98 (2003) 160; J. Comput. Biol. 8 (2001) 69; Genetics 163 (2003) 375; Genetics 111 (1985) 147) 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 that problem. An efficient algorithm does exist for the problem when the network is constrained to be a ''galled-tree'', and the ancestral sequence for the galled-tree is specified in advance (Proceedings of Second CSB Bioinformatics Conference, Los Alamitos, CA, 2003, IEEE Press, New York; J. Bioinform. Comput. Biol. 2(1) (2004) 173; INFORMS J. Comput. 16 (2004) 459). However, the more biologically realistic case is that no ancestral sequence is known in advance, and the only previous algorithmic solution for that case takes exponential time. In this paper we give an efficient solution to the galled-tree problem when no ancestral sequence is known in advance, and show that the solution produced has very strong global optimality properties. We also indicate how these results generalize to other complex biological phenomena such as gene-conversion, lateral gene transfer, hybrid speciation, and back and recurrent mutation.