Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Computers and Intractability; A Guide to the Theory of NP-Completeness
Computers and Intractability; A Guide to the Theory of NP-Completeness
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Empirical exploration of perfect phylogeny haplotyping and haplotypers
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
Influence of Tree Topology Restrictions on the Complexity of Haplotyping with Missing Data
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Haplotype Inference Constrained by Plausible Haplotype Data
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Haplotype Inference Constrained by Plausible Haplotype Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the complexity of SNP block partitioning under the perfect phylogeny model
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Connectivity is not a limit for kernelization: planar connected dominating set
LATIN'10 Proceedings of the 9th Latin American conference on Theoretical Informatics
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
Influence of tree topology restrictions on the complexity of haplotyping with missing data
Theoretical Computer Science
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Computational methods for inferring haplotype information from genotype data are used in studying the association between genomic variation and medical condition. Recently, Gusfield proposed a haplotype inference method that is based on perfect phylogeny principles. A fundamental problem arises when one tries to apply this approach in the presence of missing genotype data, which is common in practice. We show that the resulting theoretical problem is NP-hard even in very restricted cases. To cope with missing data, we introduce a variant of haplotyping via perfect phylogeny in which a path phylogeny is sought. Searching for perfect path phylogenies is strongly motivated by the characteristics of human genotype data: 70% of real instances that admit a perfect phylogeny also admit a perfect path phylogeny. Our main result is a fixed-parameter algorithm for haplotyping with missing data via perfect path phylogenies. We also present a simple linear-time algorithm for the problem on complete data.