## Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data (2002)

### Cached

### Download Links

- [compgen.bscb.cornell.edu]
- [www.cse.sc.edu]
- [www.cs.unm.edu]
- [lcbb.epfl.ch]
- [cs.unm.edu]
- [www.cse.sc.edu]
- [www.cs.utexas.edu]
- [www.cs.unm.edu]
- DBLP

### Other Repositories/Bibliography

Citations: | 29 - 14 self |

### BibTeX

@INPROCEEDINGS{Moret02inversionmedians,

author = {Bernard M. E. Moret and Adam C. Siepel and Jijun Tang and Tao Liu},

title = {Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data},

booktitle = {},

year = {2002},

pages = {521--536},

publisher = {Springer-Verlag}

}

### Years of Citing Articles

### OpenURL

### Abstract

### Citations

272 | Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals
- Hannenhalli, Pevzner
- 1995
(Show Context)
Citation Context ... GRAPPA [14], both use as their basic optimization tool an algorithm for computing the breakpoint median of three genomes. Recent work, however, based on the elegant theory of Hannenhalli and Pevzner =-=[9]-=-, has shown that inversion distance can be computed in linear time [1], a development that has allowed us to base the reconstruction process on the inversion score of a tree rather than on its breakpo... |

182 | Phylogenetic inference - Swofford, Olsen, et al. - 1996 |

95 | Genome–scale evolution: reconstructing gene orders in ancestral species
- Bourque, Pevzner
- 2002
(Show Context)
Citation Context ...e reduced the running time to just one hour on the same machine, while yielding many trees with an inversion score of 64—but with topologies identical to the previous best trees. (Bourque and Pevzner =-=[3]-=- had found one tree with a score of 65 using a somewhat different approach, while Larget et al. [11] just reported finding a number of trees that, like ours, required 64 inversions—again these trees h... |

88 |
Lengths of chromosomal segments conserved since divergence of man and
- Nadeau, Taylor
- 1984
(Show Context)
Citation Context ...G, but neither (gi,gj) nor (−gj, −gi) appear consecutively in that order in G ′ . The number of breakpoints in G relative to G ′ is the breakpoint distance between G and G ′ . The Nadeau-Tay=-=lor model [15]-=- of genome evolution, as generalized by Wang and Warnow [27], uses only genome rearrangement events, so that all genomes have equal gene content. The model assumes that each of the three types of even... |

78 | Multiple genome rearrangement and breakpoint phylogeny
- Sankoff, Blanchette
- 1998
(Show Context)
Citation Context ...t al. [2], is the most parsimonious tree with respect to breakpoint distances. The two software packages for reconstructing the breakpoint phylogeny, the original BPAnalysis of Sankoff and Blanchette =-=[21]-=- and the more recent and much faster GRAPPA [14], both use as their basic optimization tool an algorithm for computing the breakpoint median of three genomes. Recent work, however, based on the elegan... |

64 | The median problems for breakpoints are NPcomplete
- Pe’er, Shamir
- 1998
(Show Context)
Citation Context ...number of the permitted evolutionary events on the tree. This problem is NP-hard for most criteria—even the very simple problem of computing the median 1 of three genomes under such models is NP-har=-=d [4,18]-=-. All approaches to phylogeny reconstruction for such data must therefore find ways of handling significant computational difficulties. Moreover, because suboptimal solutions can yield very different ... |

61 | D.: Breakpoint phylogenies
- Blanchette, Bourque, et al.
- 1997
(Show Context)
Citation Context ...e other), a measure of distance between genomes that is independent of any particular mechanism of rearrangement, to reconstruct phylogenies; the breakpoint phylogeny, introduced by Blanchette et al. =-=[2]-=-, is the most parsimonious tree with respect to breakpoint distances. The two software packages for reconstructing the breakpoint phylogeny, the original BPAnalysis of Sankoff and Blanchette [21] and ... |

55 | A new implementation and detailed study of breakpoint analysis
- Moret, Wyman, et al.
- 2001
(Show Context)
Citation Context ...spect to breakpoint distances. The two software packages for reconstructing the breakpoint phylogeny, the original BPAnalysis of Sankoff and Blanchette [21] and the more recent and much faster GRAPPA =-=[14]-=-, both use as their basic optimization tool an algorithm for computing the breakpoint median of three genomes. Recent work, however, based on the elegant theory of Hannenhalli and Pevzner [9], has sho... |

47 | Formulations and hardness of multiple sorting by reversals
- Caprara
- 1999
(Show Context)
Citation Context ...number of the permitted evolutionary events on the tree. This problem is NP-hard for most criteria—even the very simple problem of computing the median 1 of three genomes under such models is NP-har=-=d [4,18]-=-. All approaches to phylogeny reconstruction for such data must therefore find ways of handling significant computational difficulties. Moreover, because suboptimal solutions can yield very different ... |

42 |
Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255
- RAUBESON, JANSEN
- 1992
(Show Context)
Citation Context ...an be rearranged by evolutionary events such as inversions and transpositions and, because they evolve slowly, give biologists an important new source of data for phylogeny reconstruction (see, e.g., =-=[7,16,17,19]).-=- Appropriate tools for analyzing such data may help resolve some difficult phylogenetic reconstruction problems. Developing such tools is thus an important area of research—indeed, the recent DCAF s... |

41 | Steps toward accurate reconstruction of phylogenies from gene-order data
- Moret, Tang, et al.
- 2002
(Show Context)
Citation Context ...ets and also to experiment with alternative approaches. Our program, called GRAPPA [14], includes all of the features of BPAnalysis, but is more flexible and runs up to six orders of magnitude faster =-=[12]. -=-It also allows the user to base the optimization on a tree’s inversion score or on its breakpoint score (although medians are still computed with the TSP methods of Sankoff and Blanchette, which is ... |

41 | New approaches for reconstructing phylogenies from gene order data
- Moret, Wang, et al.
- 2001
(Show Context)
Citation Context ...that has allowed us to base the reconstruction process on the inversion score of a tree rather than on its breakpoint score, with significant resulting improvements in the accuracy of reconstructions =-=[13]-=-. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances [5,23,24] (in spite of the NP-hardness of the problem). These d... |

39 |
Chloroplast DNA systematics: a review of methods and data analysis
- Olmstead, Palmer
- 1994
(Show Context)
Citation Context ...an be rearranged by evolutionary events such as inversions and transpositions and, because they evolve slowly, give biologists an important new source of data for phylogeny reconstruction (see, e.g., =-=[7,16,17,19]).-=- Appropriate tools for analyzing such data may help resolve some difficult phylogenetic reconstruction problems. Developing such tools is thus an important area of research—indeed, the recent DCAF s... |

38 |
Use of chloroplast DNA rearrangements in reconstructing plant phylogeny
- DOWNIE, PALMER
- 1992
(Show Context)
Citation Context ...an be rearranged by evolutionary events such as inversions and transpositions and, because they evolve slowly, give biologists an important new source of data for phylogeny reconstruction (see, e.g., =-=[7,16,17,19]).-=- Appropriate tools for analyzing such data may help resolve some difficult phylogenetic reconstruction problems. Developing such tools is thus an important area of research—indeed, the recent DCAF s... |

35 |
A fast linear-time algorithm for inversion distance with an experimental comparison
- Bader, Moret, et al.
(Show Context)
Citation Context ...or computing the breakpoint median of three genomes. Recent work, however, based on the elegant theory of Hannenhalli and Pevzner [9], has shown that inversion distance can be computed in linear time =-=[1]-=-, a development that has allowed us to base the reconstruction process on the inversion score of a tree rather than on its breakpoint score, with significant resulting improvements in the accuracy of ... |

30 |
Chloroplast and mitochondrial genome evolution in land plants
- Palmer
- 1992
(Show Context)
Citation Context |

29 | A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic data
- Cosner, Jansen, et al.
- 2000
(Show Context)
Citation Context ...st gene orders. Tobacco outgroup, for a total of 13 taxa, each with 105 genes. Evolutionary rates on this set appear low and most evolutionary changes are believed to have occurred through inversions =-=[6]-=-. Earlier analyses reduced the running times from an original estimate of several centuries with BPAnalysis to 9 hours on a fast workstation [12], with the best-scoring tree having an inversion score ... |

26 |
On the practical solution of the reversal median problem
- Caprara
- 2001
(Show Context)
Citation Context ... resulting improvements in the accuracy of reconstructions [13]. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances =-=[5,23,24] (-=-in spite of the NP-hardness of the problem). These developments have enabled us to extend GRAPPA by replacing the breakpoint median routine with an inversion median routine—which we conjectured 1 Th... |

26 | Genome rearrangement by reversals and insertions/deletions of contiguous segments
- El-Mabrouk
(Show Context)
Citation Context ...in the scoring of a particular tree topology as well as an important biological datum. The results we have presented here, along with other results on handling transversions and gene duplication (see =-=[8,10]-=-) justify a cautious optimism: over the next few years, the reconstruction of phylogenies from gene-order data should become applicable to much larger datasets, extending the approach from organellar ... |

25 | Finding an optimal inversion median: Experimental results
- Siepel, Moret
- 2001
(Show Context)
Citation Context ... resulting improvements in the accuracy of reconstructions [13]. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances =-=[5,23,24] (-=-in spite of the NP-hardness of the problem). These developments have enabled us to extend GRAPPA by replacing the breakpoint median routine with an inversion median routine—which we conjectured 1 Th... |

23 |
Estimating true evolutionary distances between genomes
- Wang, Warnow
- 2001
(Show Context)
Citation Context ...n that order in G ′ . The number of breakpoints in G relative to G ′ is the breakpoint distance between G and G ′ . The Nadeau-Taylor model [15] of genome evolution, as generalized by Wang and W=-=arnow [27], -=-uses only genome rearrangement events, so that all genomes have equal gene content. The model assumes that each of the three types of events obeys a Poisson distribution on each edge—with the three ... |

15 |
Transforming mice into men (polynomial algorithm for genomic distance problems
- Hannenhalli, Pevzner
- 1995
(Show Context)
Citation Context ...in the scoring of a particular tree topology as well as an important biological datum. The results we have presented here, along with other results on handling transversions and gene duplication (see =-=[8,10]-=-) justify a cautious optimism: over the next few years, the reconstruction of phylogenies from gene-order data should become applicable to much larger datasets, extending the approach from organellar ... |

10 |
P.: Genome-scale evolution: reconstructing gene orders in the ancestral species
- Guillaume, Pevzner
- 2002
(Show Context)
Citation Context ...e reduced the running time to just one hour on the same machine, while yielding many trees with an inversion score of 64—but with topologies identical to the previous best trees. (Bourque and Pevzne=-=r [3] h-=-ad found one tree with a score of 65 using a somewhat different approach, while Larget et al. [11] just reported finding a number of trees that, like ours, required 64 inversions—again these trees h... |

10 | An algorithm to find all sorting reversals
- Siepel
- 2002
(Show Context)
Citation Context ... resulting improvements in the accuracy of reconstructions [13]. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances =-=[5,23,24] (-=-in spite of the NP-hardness of the problem). These developments have enabled us to extend GRAPPA by replacing the breakpoint median routine with an inversion median routine—which we conjectured 1 Th... |

7 | Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study
- Wang, Jansen, et al.
- 2002
(Show Context)
Citation Context ...lutionary history resembling the model tree. 3.3 Labeling Internal Nodes One of the major advantages of median-based phylogeny reconstruction over alternative methods (such as the encoding methods of =-=[13,26]-=-) is that it estimates the configurations of ancestral genomes as well as the topology of the tree. The approach proposed by Sankoff and Blanchette to estimate ancestral genomes is iterative, using a ... |

5 |
Exact algorithms for the reversal median problem
- Siepel
- 2001
(Show Context)
Citation Context ...much more slowly than the algorithm for breakpoint medians) for a range of parameters that covers most organellar genomes; one by Caprara [5] and one by Siepel and Moret [24] (subsequently refined in =-=[22,23]-=-). Both algorithms use branch-andbound strategies, but the algorithm of Siepel and Moret directly searches the space of genome rearrangements for an optimal solution, using the metric property of inve... |

4 |
A Markov chain Monte Carlo approach to reconstructing ancestral genome rearrangements
- Larget, Kadane, et al.
- 2002
(Show Context)
Citation Context ...inversion score of 64—but with topologies identical to the previous best trees. (Bourque and Pevzner [3] had found one tree with a score of 65 using a somewhat different approach, while Larget et al=-=. [11] j-=-ust reported finding a number of trees that, like ours, required 64 inversions—again these trees have the same topologies as our previous best trees.) While the inversion median routine itself was m... |

2 |
Inferring phylogenetic relationships using whole genome data: A case study of photosynthetic organelles and chloroplast genomes
- Raubeson, Moret, et al.
- 2001
(Show Context)
Citation Context ...akpoint medians (a pruning rate of 99.94%). Our second set has 11 taxa (including land plants as well as red and green algae), each with 33 genes. This set was also analyzed with a variety of methods =-=[20]-=-; unlike the Campanulaceae set, it has high divergence, with intertaxa inversion distances averaging over 10. The analyses of [20] used a variety of techniques, including GRAPPA with breakpoint median... |