Reconstructing a history of recombinations from a set of sequences
SODA '94 Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms
Introduction to algorithms
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
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Genotype Sequence Segmentation: Handling Constraints and Noise
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Efficiently finding the most parsimonious phylogenetic tree via linear programming
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
On the complexity of SNP block partitioning under the perfect phylogeny model
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
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
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Dynamic visualization and comparative analysis of multiple collinear genomic data
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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Intraspecific genomes can be subdivided into blocks with limited diversity. Understanding the distribution and structure of these blocks will help to unravel many biological problems including the identification of genes associated with complex diseases, finding the ancestral origins of a given population, and localizing regions of historical recombination, gene conversion, and homoplasy. We present methods for partitioning a genome into blocks for which there are no apparent recombinations, thus providing parsimonious sets of compatible genome intervals based on the four-gamete test. Our contribution is a thorough analysis of the problem of dividing a genome into compatible intervals, in terms of its computational complexity, and by providing an achievable lower-bound on the minimal number of intervals required to cover an entire data set. In general, such minimal interval partitions are not unique. However, we identify properties that are common to every possible solution. We also define the notion of an interval set that achieves the interval lower-bound, yet maximizes interval overlap. We demonstrate algorithms for partitioning both haplotype data from inbred mice as well as outbred heterozygous genotype data using extensions of the standard four-gamete test. These methods allow our algorithms to be applied to a wide range of genomic data sets.