Tabu Search
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Metaheuristics in combinatorial optimization: Overview and conceptual comparison
ACM Computing Surveys (CSUR)
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
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
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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The problem of inferring ancestral genetic information in terms of a set of founders of a given population arises in various biological contexts. In optimization terms, this problem can be formulated as a combinatorial string problem. The main problem of existing techniques, both exact and heuristic, is that their time complexity scales exponentially, which makes them impractical for solving large-scale instances. We developed a new constructive heuristic and a tabu search method with the explicit aim of providing solutions in a reduced amount of computation time. Experimental results show that when the number of founders grows, our algorithms have advantages over the ones proposed in the literature.