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
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
A New Approach for Approximating the Transposition Distance
SPIRE '00 Proceedings of the Seventh International Symposium on String Processing Information Retrieval (SPIRE'00)
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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Given the gene-order of a set of contemporary genomes, the problem of recovering the rearrangement scenario that best explains these arrangements can be challenging even if the phylogeny of these species is known. Most of the existing methods can identify an optimal or near-optimal scenario in terms of parsimony but they cannot distinguish between reliable and putative events on the reconstructed tree. In this paper, we propose an efficient method to infer partial rearrangement scenarios consisting of only reliable ancestral events. Using simulations, we show that the approach allows the recovery of actual events with high sensitivity and specificity under both random and fragile rearrangement models. Finally, we also apply the approach to two real data sets.