Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
The Haplotyping problem: an overview of computational models and solutions
Journal of Computer Science and Technology
Integer Programming Approaches to Haplotype Inference by Pure Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Solving haplotyping inference parsimony problem using a new basic polynomial formulation
Computers & Mathematics with Applications
On the asymmetric representatives formulation for the vertex coloring problem
Discrete Applied Mathematics
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
A polynomial case of the parsimony haplotyping problem
Operations Research Letters
A Decomposition of the Pure Parsimony Haplotyping Problem
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Computers and Operations Research
Estimating population size via line graph reconstruction
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Efficient symmetry breaking formulations for the job grouping problem
Computers and Operations Research
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Haplotyping estimation from aligned single nucleotide polymorphism fragments has attracted increasing attention in recent years because of its importance in the analysis of fine-scale genetic data. Its application fields range from mapping of complex disease genes to inferring population histories, passing through designing drugs, functional genomics, and pharmacogenetics. The literature proposes several criteria for haplotyping populations, each of them characterized by biological motivations. One of the most important haplotyping criteria is parsimony, which consists of finding the minimum number of haplotypes necessary to explain a given set of genotypes. Parsimonious haplotype estimation is an NP-hard problem for which the literature has proposed several integer programming (IP) models. Here, we describe a new polynomial-sized IP model based on the concept of class representatives, already used for the coloring problem. We propose valid inequalities to strengthen our model and show, through computational experiments, that our model outperforms the best IP models currently known in literature.