The hardness of approximation: gap location
Computational Complexity
A Linear-Time Algorithm for Finding Tree-Decompositions of Small Treewidth
SIAM Journal on Computing
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Islands of Tractability for Parsimony Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotype inference using a genetic algorithm
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Phylogenetic network inferences through efficient haplotyping
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
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We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.