Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Haplotypes histories as pathways of recombinations
Bioinformatics
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
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
Recombinomics: population genomics from a recombination perspective
Proceedings of the Third C* Conference on Computer Science and Software Engineering
Genome-wide compatible SNP intervals and their properties
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Bounds on the minimum mosaic of population sequences under recombination
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
A randomized iterated greedy algorithm for the founder sequence reconstruction problem
LION'10 Proceedings of the 4th international conference on Learning and intelligent optimization
Large neighbourhood search algorithms for the founder sequence reconstruction problem
Computers and Operations Research
Haplotype inference via hierarchical genotype parsing
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Hybrid metaheuristics in combinatorial optimization: a tutorial
TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
Minimum mosaic inference of a set of recombinants
CATS '11 Proceedings of the Seventeenth Computing: The Australasian Theory Symposium - Volume 119
Minimum mosaic inference of a set of recombinants
CATS 2011 Proceedings of the Seventeenth Computing on The Australasian Theory Symposium - Volume 119
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Detecting historical recombination is an important computational problem which has received great attention recently. Due to recombination, input sequences form a mosaic, where each input sequence is composed of segments from founder sequences. In this paper, we present improved algorithms for the problem of finding the minimum mosaic (a mosaic containing the fewest ancestral segments) of a set of recombinant sequences. This problem was first formulated in [15], where an exponential-time algorithm was described. It is also known that a restricted version of this problem (assuming recombination occurs only at predefined block boundaries) can be solved in polynomial time [15,11]. We give a polynomial-time algorithm for a special case of the minimum (blockless) mosaic problem, and a practical algorithm for the general case. Experiments with our method show that it is practical in a range of data much larger than could be handled by the algorithm described in [15].