Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Incomplete Directed Perfect Phylogeny
SIAM Journal on Computing
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
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Improved recombination lower bounds for haplotype data
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Constructing majority-rule supertrees
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On a conjecture about compatibility of multi-states characters
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Efficiently solvable perfect phylogeny problems on binary and k-state data with missing values
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Identifying rogue taxa through reduced consensus: NP-Hardness and exact algorithms
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Efficient enumeration of the directed binary perfect phylogenies from incomplete data
SEA'12 Proceedings of the 11th international conference on Experimental Algorithms
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Several central and well-known combinatorial problems in phylogenetics and population genetics have efficient, elegant solutions when the input is complete or consists of haplotype data, but lack efficient solutions when input is either incomplete, consists of genotype data, or is for problems generalized from decision questions to optimization questions. Unfortunately, in biological applications, these harder problems arise very often. Previous research has shown that integer-linear programming can sometimes be used to solve hard problems in practice on a range of data that is realistic for current biological applications. Here, we describe a set of related integer linear programming (ILP) formulations for several additional problems, most of which are known to be NP-hard. These ILP formulations address either the issue of missing data, or solve Haplotype Inference Problems with objective functions that model more complex biological phenomena than previous formulations. These ILP formulations solve efficiently on data whose composition reflects a range of data of current biological interest. We also assess the biological quality of the ILP solutions: some of the problems, although not all, solve with excellent quality. These results give a practical way to solve instances of some central, hard biological problems, and give practical ways to assess how well certain natural objective functions reflect complex biological phenomena. Perl code to generate the ILPs (for input to CPLEX) is on the web at wwwcsif.cs.ucdavis.edu/˜gusfield.