Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Incomplete Directed Perfect Phylogeny
SIAM Journal on Computing
An Efficient Algorithm for Perfect Phylogeny Haplotyping
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
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
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
Influence of Tree Topology Restrictions on the Complexity of Haplotyping with Missing Data
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Efficiently solvable perfect phylogeny problems on binary and k-state data with missing values
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Influence of tree topology restrictions on the complexity of haplotyping with missing data
Theoretical Computer Science
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The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of haplotypes or genotypes with missing entries. The earlier approaches for both of these problems dealt with restricted versions of the problems, where the root is either available or can be trivially re-constructed from the data, or certain assumptions were made about the data. In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor trivially recoverable from the data. Both IPP and IPPH problems have previously been proven to be NPcomplete. Here, we present efficient enumerative algorithms that can handle practical instances of the problem. Empirical analysis on simulated data shows that the algorithms perform very well both in terms of speed and in terms accuracy of the recovered data.