An almost linear-time algorithm for graph realization
Mathematics of Operations Research
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
The Haplotyping problem: an overview of computational models and solutions
Journal of Computer Science and Technology
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
Combinatorial problems arising in SNP and haplotype analysis
DMTCS'03 Proceedings of the 4th international conference on Discrete mathematics and theoretical computer science
An Efficient Algorithm for Perfect Phylogeny Haplotyping
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
The phasing of heterozygous traits: Algorithms and complexity
Computers & Mathematics with Applications
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Boosting Haplotype Inference with Local Search
Constraints
Haplotyping for Disease Association: A Combinatorial Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Undirected Incomplete Perfect Phylogeny Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genome-wide compatible SNP intervals and their properties
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Phylogenetic network inferences through efficient haplotyping
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
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Since the introduction of the Perfect Phylogeny Haplotyping (PPH) Problem in Recomb 2002 [15], the problem of finding a linear-time (deterministic, worst-case) solution for it has remained open, despite broad interest in the PPH problem and a series of papers on various aspects of it. In this paper we solve the open problem, giving a practical, deterministic linear-time algorithm based on a simple data-structure and simple operations on it. The method is straightforward to program and has been fully implemented. Simulations show that it is much faster in practice than prior methods. The value of a linear-time solution to the PPH problem is partly conceptual and partly for use in the inner-loop of algorithms for more complex problems, where the PPH problem must be solved repeatedly.