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
Probability models for genome rearrangement and linear invariants for phylogenetic inference
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Sorting permutations by tanspositions
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Estimating true evolutionary distances between genomes
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
High-Performance Algorithm Engineering for Computational Phylogenetics
ICCS '01 Proceedings of the International Conference on Computational Science-Part II
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics
Experimental algorithmics
Reversal and transposition medians
Theoretical Computer Science
Approximating the true evolutionary distance between two genomes
Journal of Experimental Algorithmics (JEA)
Improving tree search in phylogenetic reconstruction from genome rearrangement data
WEA'07 Proceedings of the 6th international conference on Experimental algorithms
Evolution of tandemly arrayed genes in multiple species
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
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
Bootstrapping phylogenies inferred from rearrangement data
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Constructing camin-sokal phylogenies via answer set programming
LPAR'06 Proceedings of the 13th international conference on Logic for Programming, Artificial Intelligence, and Reasoning
Quartet-based phylogeny reconstruction from gene orders
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Linear programming for phylogenetic reconstruction based on gene rearrangements
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have also further improved the running time of our GRAPPA software suite through a combination of tighter bounding and better use of the bounds. We present new experimental results (that extend those we presented at ISMB'01 and WABI'01) that demonstrate the accuracy and robustness of our distance estimators under a wide range of model conditions. Moreover, using the best of our distance estimators (EDE) in our GRAPPA software suite, along with more sophisticated bounding techniques, produced spectacular improvements in the already huge speedup: whereas our earlier experiments showed a one-million-fold speedup (when run on a 512-processor cluster), our latest experiments demonstrate a speedup of one hundred million. The combination of these various advances enabled us to conduct new phylogenetic analyses of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and confirming that inversion can be viewed as the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.