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## Breakpoint phylogenies (1997)

Citations: | 70 - 4 self |

### Citations

103 | Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement
- Kececioglu, Sankoff
- 1995
(Show Context)
Citation Context ...ility of the \true" history of genomic divergence { in fact, there is a proliferation of of optimal edit paths (and severe underestimation of the total number of events generating the divergence, cf. =-=[5]-=-) for moderate or large gene-order distances. These problems all militate in favour of extending gene-order comparisons to three or more genomes through a much simpler and model-free metric, namely th... |

99 |
Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome
- Sankoff, Leduc, et al.
- 1992
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Citation Context ...1 Introduction There have been a number of investigations of phylogeny of N > 2 genomes based on the pairwise comparison of the gene orders of these genomes, followed by distance matrix methods (e.g. =-=[8]-=-). Treeing methods based on the direct comparison of all N gene orders, which infer gene order at ancestral nodes [4, 9], have been little used because of the di culty ingeneralizing measures of genom... |

56 | Parametric genome rearrangement.
- Blanchette, Kunisawa, et al.
- 1996
(Show Context)
Citation Context ...f reconstructing evolutionary history. This include unwarranted assumptions as to the relative importance (i.e. costs) of reversals, transpositions, translocations and other rearrangement events (cf. =-=[1]) and the -=-fallacy that calculation of an edit distance allows the recoverability of the "true" history of genomic divergence -- in fact, there is a proliferation of of optimal edit paths (and severe u... |

55 | The median problem for breakpoints in comparative genomics. In:
- Sankoff, Blanchette
- 1997
(Show Context)
Citation Context ..., B and C, containing the genes in #, we want to find median(A,B,C), a genome S containing the genes in # such that #(S, A) + #(S, B) + #(S, C) is minimized. This can be reduced to the TSP as follows =-=[2]-=-. We define # to be the complete graph whose vertices are the elements of #. For each edge gh in E(#), let u(gh) be the number of times g and h are adjacent in the three genomes. Set w(gh) = 3 - u(gh)... |

45 | Genome sequence comparison and scenarios for gene rearrangements: a test case.
- Hannenhalli, Chappey, et al.
- 1995
(Show Context)
Citation Context ...son of the gene orders of these genomes, followed by distance matrix methods (e.g. [8]). Treeing methods based on the direct comparison of all N gene orders, which infer gene order at ancestral nodes =-=[4, 9]-=-, have been little used because of the di culty ingeneralizing measures of genomic distance to more than two genomes { there are no algorithms available, aside from rough heuristics, for handling even... |

41 |
Frequency of insertion-deletion, transversion, and transition in evolution of 5S ribosomal RNA.
- SANKOFF, CEDERGREN, et al.
- 1976
(Show Context)
Citation Context ...ian Algorithm Applied Iteratively to Phylogeny Decomposed into Overlapping Triples. A general method for the inference of ancestral genomes on a xed binary tree is the iterative improvement method of =-=[7]-=-, as adapted for the genomics context in [9, 3]. Each of the N 0 2 internal vertices, together with its three neighbors, de nes a 3-star. The solution to the Steiner point problem will have areconstru... |

30 | Original synteny
- Ferretti, Nadeau, et al.
- 1996
(Show Context)
Citation Context ...ny Decomposed into Overlapping Triples. A general method for the inference of ancestral genomes on a xed binary tree is the iterative improvement method of [7], as adapted for the genomics context in =-=[9, 3]-=-. Each of the N 0 2 internal vertices, together with its three neighbors, de nes a 3-star. The solution to the Steiner point problem will have areconstructed genome associated with each such vertex, w... |

19 | Steiner points in the space of genome rearrangements.
- Sankoff, Sundaram, et al.
- 1996
(Show Context)
Citation Context ...son of the gene orders of these genomes, followed by distance matrix methods (e.g. [8]). Treeing methods based on the direct comparison of all N gene orders, which infer gene order at ancestral nodes =-=[4, 9]-=-, have been little used because of the di culty ingeneralizing measures of genomic distance to more than two genomes { there are no algorithms available, aside from rough heuristics, for handling even... |

1 |
Multiple genome rearrangement," Manuscript, Centre de recherches mathematiques
- D, Blanchette
- 1997
(Show Context)
Citation Context ...s to assess how frequently the methods are likely to achieve global optima. We havefound at what point parsimony leads to underestimation of the number of events generating the data. In another paper =-=[6]-=-, we analyze the multiplicity ofequivalent local minima and the breakpoint distances amongst them, as an assessment of the reliability of reconstructed gene orders. An important assumption in this wor... |