Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Large scale reconstruction of haplotypes from genotype data
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Journal of Computer and System Sciences - Special issue on bioinformatics II
Empirical exploration of perfect phylogeny haplotyping and haplotypers
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotype Inferring Via Galled-Tree Networks Is NP-Complete
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Discrete Applied Mathematics
Haplotype Inference Constrained by Plausible Haplotype Data
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Algorithm for haplotype inferring via galled-tree networks with simple galls
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
SplittingHeirs: inferring haplotypes by optimizing resultant dense graphs
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Haplotype Inference Constrained by Plausible Haplotype Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogenetic network inferences through efficient haplotyping
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
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The haplotype inference (HI) problem is the problem of inferring 2n haplotype pairs from n observed genotype vectors. This is a key problem that arises in studying genetic variation in populations, for example in the ongoing HapMap project [5]. In order to have a hope of finding the haplotypes that actually generated the observed genotypes, we must use some (implicit or explicit) genetic model of the evolution of the underlying haplotypes. The Perfect Phylogeny Haplotyping (PPH) model was introduced in 2002 [9] to reflect the “neutral coalescent” or “perfect phylogeny” model of haplotype evolution. The PPH problem (which can be solved in polynomial time) is to determine whether there is an HI solution where the inferred haplotypes can be derived on a perfect phylogeny (tree). Since the introduction of the PPH model, several extensions and modifications of the PPH model have been examined. The most important modification, to model biological reality better, is to allow a limited number of biological events that violate the perfect phylogeny model. This was accomplished implicitly in [7,12] with the inclusion of several heuristics into an algorithm for the PPH problem [8]. Those heuristics are invoked when the genotype data cannot be explained with haplotypes that fit the perfect phylogeny model. In this paper, we address the issue explicitly, by allowing one recombination or homoplasy event in the model of haplotype evolution. We formalize the problems and provide a polynomial time solution for one problem, using an additional, empirically-supported assumption. We present a related framework for the second problem which gives a practical algorithm. We believe the second problem can be solved in polynomial time.