STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Reconstructing a history of recombinations from a set of sequences
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Genotype Sequence Segmentation: Handling Constraints and Noise
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Tabu Search for the Founder Sequence Reconstruction Problem: A Preliminary Study
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Bounds on the minimum mosaic of population sequences under recombination
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Haplotype inference via hierarchical genotype parsing
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Large neighbourhood search algorithms for the founder sequence reconstruction problem
Computers and Operations Research
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In this paper, we investigate the central problem of finding recombination events (Kececioglu & Gusfield 1998, Ukkonen 2002, Schwartz et al. 2002, Koivisto et al. 2004, Rastas & Ukkonen 2007, Wu & Gusfield 2007). It is commonly assumed that a present population is a descendent of a small number of specific sequences called founders. Due to recombination, a present sequence (called a recombinant) is thus composed of blocks from the founders. A major question related to founder sequences is the so-called Minimum Mosaic problem: using the natural parsimony criterion for the number of recombinations, find the "best" founders. In this article, we prove that the Minimum Mosaic problem given haplotype recombinants with no missing values is hard for an unbounded number of founders and propose some exact exponential-time algorithms for the problem. Notice that, in (Rastas & Ukkonen 2007), Rastas et al. proved that the Minimum Mosaic problem is hard using a somewhat unrealistic mutation cost function (details provided afterwards). The aim of this paper is to provide a better complexity insight of the problem.