Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Islands of Tractability for Parsimony Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotyping with missing data via perfect path phylogenies
Discrete Applied Mathematics
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Undirected Incomplete Perfect Phylogeny Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A polynomial case of the parsimony haplotyping problem
Operations Research Letters
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
Phylogeny - and parsimony-based haplotype inference with constraints
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
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 based on genotype data. This problem, which has strong practical applications, can be approached using both statistical as well as combinatorial methods. While the most direct combinatorial approach, maximum parsimony, leads to NP-complete problems, the perfect phylogeny model proposed by Gusfield yields a problem, called pph, that can be solved in polynomial (even linear) time. Even this may not be fast enough when the whole genome is studied, leading to the question of whether parallel algorithms can be used to solve the pphproblem. In the present paper we answer this question affirmatively, but we also give lower complexity bounds on its complexity. In detail, we show that the problem lies in Mod2L, a subclass of the circuit complexity class NC2, and is hard for logarithmic space and thus presumably not in NC1. We also investigate variants of the pphproblem that have been studied in the literature, like the perfect path phylogeny haplotyping problem and the combined problem where a perfect phylogeny of maximal parsimony is sought, and show that some of these variants are TC0-complete or lie in AC0.