Phylogeny - and parsimony-based haplotype inference with constraints

Authors:
Michael Elberfeld;Till Tantau
Affiliations:
Institut für Theoretische Informatik, Universität zu Lübeck, Lübeck, Germany;Institut für Theoretische Informatik, Universität zu Lübeck, Lübeck, Germany
Venue:
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Year:
2010

Citing 9
Cited 1

Haplotyping as perfect phylogeny: conceptual framework and efficient solutions

Proceedings of the sixth annual international conference on Computational biology
Integer Programming Approaches to Haplotype Inference by Pure Parsimony

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Islands of Tractability for Parsimony Haplotyping

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms

INFORMS Journal on Computing
A Linear-Time Algorithm for the Perfect Phylogeny Haplotype Problem

Algorithmica
Shorelines of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems

MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
Haplotype Inference Constrained by Plausible Haplotype Data

CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Haplotype inference by pure Parsimony

CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching

Haplotype Inference Constrained by Plausible Haplotype Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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Abstract

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their CPM 2009 paper, Fellows et al. studied an extension of this approach that incorporates prior knowledge in the form of a set of candidate haplotypes from which the right haplotypes must be chosen. While this approach may help to increase the accuracy of haplotyping methods, it was conjectured that the resulting formal problem constrained perfect phylogeny haplotyping might be NP-complete. In the present paper we present a polynomial-time algorithm for it. Our algorithmic ideas also yield new fixed-parameter algorithms for related haplotyping problems based on the maximum parsimony assumption.