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
Probability models for genome rearrangement and linear invariants for phylogenetic inference
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Hybrid tree reconstruction methods
Journal of Experimental Algorithmics (JEA)
High-Performance Algorithm Engineering for Computational Phylogenetics
The Journal of Supercomputing - Special issue on computational issues in fluid dynamics optimization and simulation
Steps toward accurate reconstructions of phylogenies from gene-order data
Journal of Computer and System Sciences - Computational biology 2002
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes
WABI '01 Proceedings of the First 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
Genome Rearrangement Phylogeny Using Weighbor
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Assignment of Orthologous Genes via Genome Rearrangement
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Comparing bacterial genomes from linear orders of patterns
Discrete Applied Mathematics
Expected number of breakpoints after t random reversals in genomes with duplicate genes
Discrete Applied Mathematics
Baculovirus phylogeny based on genome rearrangements
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Bootstrapping phylogenies inferred from rearrangement data
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
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Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees in these models [3, 6, 7, 15, 17]. A necessary component of any such method is the ability to accurately estimate true evolutionary distances between two genomes, which is the number of rearrangement events that took place in the evolutionary history between them. We present a new technique called IEBP, for estimating the true evolutionary distance between two genomes, whether signed or unsigned, circular or linear, and for any relative probabilities of rearrangement event classes. The method is highly accurate, as our simulation study shows. This simulation study also shows that the distance estimation technique improves the accuracy of the phylogenetic trees reconstructed by the popular distance-based method, neighbor joining [1, 20].