SIAM Journal on Discrete Mathematics
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Concrete Mathematics: A Foundation for Computer Science
Concrete Mathematics: A Foundation for Computer Science
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
(1 + ɛ)-Approximation of sorting by reversals and transpositions
Theoretical Computer Science
On the Approximation Properties of Independent Set Problem in Degree 3 Graphs
WADS '95 Proceedings of the 4th International Workshop on Algorithms and Data Structures
Approximating the Expected Number of Inversions Given the Number of Breakpoints
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
A Very Elementary Presentation of the Hannenhalli-Pevzner Theory
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Improving inversion median computation using commuting reversals and cycle information
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Reactive stochastic local search algorithms for the genomic median problem
EvoCOP'08 Proceedings of the 8th European conference on Evolutionary computation in combinatorial optimization
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
The transposition median problem is NP-complete
Theoretical Computer Science
A practical algorithm for ancestral rearrangement reconstruction
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
| Hi-index | 5.23 |
In determining phylogenetic trees using gene order information, medians provide a powerful alternative to pairwise distances. On the other hand, both breakpoint and reversal medians are NP-hard to compute and the use of medians has been limited to relatively closely related genomes. In this paper, we show that in spite of the greater non-uniqueness of reversal medians, compared to breakpoint medians, medians of moderately distant genomes are often widely spread. This means that regardless of which approximation algorithms one may devise for computing reversal medians, the genomes need to be closely related for phylogenetic tree computations to be successful. To show this, we use results on transposition medians, which behave similarly, and also support our claims with simulations and a real data example with widely spread medians.