Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
The complexity of satisfiability problems
STOC '78 Proceedings of the tenth annual ACM symposium on Theory of computing
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)
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
Parameterized Complexity
Hi-index | 5.23 |
Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast haplotyping method is based on an evolutionary model in which a perfect phylogenetic tree is sought that explains the observed data. Unfortunately, when data entries are missing, which is often the case in laboratory data, the resulting formal problem ipph, which stands for incomplete perfect phylogeny haplotyping, is NP-complete. 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, at least, a fixed-parameter algorithm is known. Such drastic and ad hoc simplifications turn out to be unnecessary to make ipph tractable: we present the first theoretical analysis of a parameterized algorithm, which we develop in the course of the paper, that works for arbitrary instances of ipph. This tractability result is optimal insofar as we prove ipph to be NP-complete whenever any of the parameters we consider is not fixed, but part of the input.