Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Hardness of Approximating Problems on Cubic Graphs
CIAC '97 Proceedings of the Third Italian Conference on Algorithms and Complexity
Journal of Functional Programming
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)
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
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A polynomial case of the parsimony haplotyping problem
Operations Research Letters
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
Pure Parsimony Xor Haplotyping
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Phylogeny - and parsimony-based haplotype inference with constraints
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Extended islands of tractability for parsimony haplotyping
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Pure Parsimony Xor Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
Graphs of separability at most 2
Discrete Applied Mathematics
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The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the haplotypes to be embedded in a perfect phylogeny, an evolutionary tree with biologically-motivated restrictions. For PH, we extend recent work by further mapping the interface between ``easy'' and ``hard'' instances, within the framework of (k,l)-bounded instances where the number of 2's per column and row of the input matrix is restricted. By exploring, in the same way, the tractability frontier of MPPH we provide the first concrete, positive results for this problem. In addition, we construct for both PH and MPPH polynomial time approximation algorithms, based on properties of the columns of the input matrix.