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)
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Improved bounds on sorting with length-weighted reversals
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
A very elementary presentation of the Hannenhalli-Pevzner theory
Discrete Applied Mathematics
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A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (aka inversions) and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process — including both the tree-topology as well as internal node genome orders — is uniquely determined, a property that is of major significance both in theory and in practice. Furthermore, the repeats are employed to provide linear-time algorithms for reconstructing both the genomic orders and the phylogeny, which are NP-hard problems under the classical model of sorting by reversals (SBR).