An Efficient Algorithm for Perfect Phylogeny Haplotyping

Authors:
Ravi VijayaSatya;Amar Mukherjee
Affiliations:
University of Central Florida;University of Central Florida
Venue:
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Year:
2005

Citing 4
Cited 2

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
The Haplotyping problem: an overview of computational models and solutions

Journal of Computer Science and Technology
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

The Undirected Incomplete Perfect Phylogeny Problem

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the genealogy of asexual diploids

RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology

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Abstract

The Perfect Phylogeny Haplotyping (PPH) problem is one of the many computational approaches to the Haplotype Inference (HI) problem. Though there are many O(nm虏) solutions to the PPH problem, the complexity of the PPH problem itself has remained an open question. In this paper, We introduce the FlexTree data structure that represents all the solutions for a PPH instance. We also introduce row-ordering that arranges the genotypes in a more manageable fashion. The column ordering, the FlexTree data structure and the row ordering together make the O(nm) OPPH algorithm possible. We also present some results on simulated data which demonstrate that the OPPH algorithm performs quiet impressively when compared to the earlier O(nm虏) algorithms.