Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
WADS '01 Proceedings of the 7th International Workshop on Algorithms and Data Structures
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
The transposition median problem is NP-complete
Theoretical Computer Science
A special-purpose architecture for solving the breakpoint median problem
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
A practical algorithm for ancestral rearrangement reconstruction
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
GASTS: parsimony scoring under rearrangements
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
A parallel algorithm for solving the reversal median problem
PPAM'05 Proceedings of the 6th international conference on Parallel Processing and Applied Mathematics
The reversal median problem, common intervals, and mitochondrial gene orders
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
The median problem for the reversal distance in circular bacterial genomes
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Linear programming for phylogenetic reconstruction based on gene rearrangements
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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We derive a branch-and-bound algorithm to find an optimal inversion median of three signed permutations. The algorithm prunes to manageable size an extremely large search tree using simple geometric properties of the problem and a newly available linear-time routine for inversion distance. Our experiments on simulated data sets indicate that the algorithm finds optimal medians in reasonable time for genomes of medium size when distances are not too large, as commonly occurs in phylogeny reconstruction. In addition, we have compared inversion and breakpoint medians, and found that inversion medians generally score significantly better and tend to be far more unique, which should make them valuable in median-based tree-building algorithms.