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'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Phylogeny - and parsimony-based haplotype inference with constraints
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
Influence of tree topology restrictions on the complexity of haplotyping with missing data
Theoretical Computer Science
The binary perfect phylogeny with persistent characters
Theoretical Computer Science
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The inference of evolutionary trees from binary species-character matrices is a fundamental computational problem in classical phylogenetic studies. Several problems arising in this field lead to different variants of the inference problem; some of these concern input data with missing values or incomplete matrices. A model of inference from incomplete data that has recently gained a remarkable interest is the Perfect Phylogeny Haplotype problem (PPH) introduced in [1] and successfully applied to infer haplotypes from genotype data. A stated open issue in this research field is the linear-time solution of this inference problem. In this paper we solve this question and give an O(nm)-time algorithm to complete matrices of n rows and m columns to represent PPH solutions: we show that solving the problem requires recognizing special posets of width 2.