Linear time algorithms for NP-hard problems restricted to partial k-trees
Discrete Applied Mathematics
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
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Maximum likelihood resolution of multi-block genotypes
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Islands of Tractability for Parsimony Haplotyping
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th 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
A fundamental decomposition theory for phylogenetic networks and incompatible characters
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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
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The genotype phasing problem is to determine the haplotypes of diploid individuals from their genotypes where linkage relationships are not known. Based on the model of perfect phylogeny, the genotype phasing problem can be solved in linear time. However, recombinations may occur and the perfect phylogeny model thus cannot interpret genotype data with recombinations. This paper develops a graph theoretical approach that can reduce the problem to finding a subgraph pattern contained in a given graph. Based on ordered graph tree decomposition, this problem can be solved efficiently with a parameterized algorithm. Our tests on biological genotype data showed that this algorithm is extremely efficient and its interpretation accuracy is better than or comparable with that of other approaches.