Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Incomplete Directed Perfect Phylogeny
SIAM Journal on Computing
Haplotyping with missing data via perfect path phylogenies
Discrete Applied Mathematics
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
The Undirected Incomplete Perfect Phylogeny Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes from genotype data. One fast haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. Unfortunately, when data entries are missing as is often the case in laboratory data, the resulting incomplete perfect phylogeny haplotyping problem ipph is NP-complete and no theoretical results are known concerning its approximability, fixed-parameter tractability, or exact algorithms for it. Even radically simplified versions, such as the restriction to phylogenetic trees consisting of just two directed paths from a given root, are still NP-complete; but here a fixed-parameter algorithm is known. We show that such drastic and ad hoc simplifications are not necessary to make ipph fixed-parameter tractable: We present the first theoretical analysis of an algorithm, which we develop in the course of the paper, that works for arbitrary instances of ipph . On the negative side we show that restricting the topology of perfect phylogenies does not always reduce the computational complexity: while the incomplete directed perfect phylogeny problem is well-known to be solvable in polynomial time, we show that the same problem restricted to path topologies is NP-complete.