Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Model-based inference of haplotype block variation
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Maximum likelihood resolution of multi-block genotypes
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Joint discovery of haplotype blocks and complex trait associations from SNP sequences
UAI '04 Proceedings of the 20th conference on Uncertainty in artificial intelligence
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Fast Bayesian Haplotype Inference Via Context Tree Weighting
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Artificial Intelligence in Medicine
Haplotype Inference Constrained by Plausible Haplotype Data
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Probabilistic logic learning from haplotype data
Probabilistic inductive logic programming
Bounds on the minimum mosaic of population sequences under recombination
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
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
Indexing a dictionary for subset matching queries
Algorithms and Applications
Haplotype inference via hierarchical genotype parsing
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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We give a new algorithm for the genotype phasing problem. Our solution is based on a hidden Markov model for haplotypes. The model has a uniform structure, unlike most solutions proposed so far that model recombinations using haplotype blocks. In our model, the haplotypes can be seen as a result of iterated recombinations applied on a few founder haplotypes. We find maximum likelihood model of this type by using the EM algorithm. We show how to solve the subtleties of the EM algorithm that arise when genotypes are generated using a haplotype model. We compare our method to the well-known currently available algorithms (phase, hap, gerbil) using some standard and new datasets. Our algorithm is relatively fast and gives results that are always best or second best among the methods compared.