M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman, "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes," in Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB00), pp. 104--115, (San Diego, CA), 2000.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....improved it and gave a nk ) algorithm. References available on request. As we can see, this is just the tip of the iceberg. I have not even mentioned other combinatorial problems related to, for 9 instance, breakpoint phylogenies (see Blanchette, Bourque and Sankoff [BBS97] Coster et al. [CJMRWWW00], B. Moret et al. MWBWY01] and Fellows [Fe03] or combinatorial sequence alignment (see, e.g. Bodlaender et al. BDFHW95] An excellent recent real FPT analysis for breakpoints can be found in Gramm and Niedermeier [GN02] There are myriads of natural parameters in computational biology. ....

M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow and S. Wyman, "A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental P hylogenetic Analyses of Real and Synthetic Data," in: Proceedings of the 8th International Conf. o n Intelligent Systems for Molecular Biology (ISMB 2000), San Diego, 2000, pp. 104-- 115.

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M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman, "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes," in Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB00), pp. 104--115, (San Diego, CA), 2000.

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M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

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M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

....genomes that we had previously analyzed using a variety of methods. Our first set contains 12 Campanulaceae plus a 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 of 67. Running the same code with the inversion median routine reduced the running time to just ....

M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

....by reversals [2,12] and a linear time algorithm for computing inversion distances [1] Note that signed permutations correspond to genomes for which the direction of transcription of each gene is known as well as the ordering of the genes. Much recent work on rearrangement based phylogeny [ 5,6,14,15,18] stems from an algorithm by Sankoff and Blanchette [ 17] that iterates over a prospective tree, repeatedly finds medians of the three permutations adjacent to each internal vertex, and uses them to improve the tree until convergence occurs. This method finds locally optimal trees and ....

M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology ISMB-2000, pages 104--115, 2000.

....tree thus denote evolutionary relationships. Due to difficulties in rooting the trees, these phylogenies are usually (but not always) represented by unrooted leaf labelled trees. Figure 1 shows two proposed phylogenies, one for several species of the Campanulaceae (bluebell flower) family (from [10]) and the other for herpesviruses that are known to affect humans (from [8] Note that the Campanulaceae tree is rooted through the use of a distantly related species (here tobacco) called an outgroup in this context (the root is taken to be the internal node to which the outgroup is attached) ....

.... suggested that this approach works well for certain datasets (i.e. it obtains trees that are close to the model tree) but that the implementation developed by Sankoff and Blanchette, the BPAnalysis software [33] is too slow to be used on anything other than small datasets with a few genes [9, 10]. 4.1 Breakpoint Analysis: Details When each genome has the same set of genes and each gene appears exactly once, a genome can be described by an ordering (circular or linear) of these genes, each gene given with an orientation that is either positive (g i ) or negative ( g i ) Given two ....

M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proceedings of the 8th Int'l Conference on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

....various heuristics for the breakpoint phylogeny. We reimplemented and extended their approach in our GRAPPA [17] software, which runs several orders of magnitude faster thanks to algorithm engineering techniques [24] Other heuristics for solving the breakpoint phylogeny problem have been proposed [8, 12, 13]. Rather than attempting to derive the most parsimonious trees (or an approximation thereof) we can use existing distance based methods, such as neighbor joining (NJ) 30] perhaps the most popular phylogenetic method) in conjunction with methods for defining leaf to leaf distances in the ....

M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

....breakpoint medians using inversion medians Fig. 2. Phylogenies of 11 plants based on chloroplast 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 of 67. Running the same code with the inversion median routine reduced the running time to just ....

M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104--115, 2000.

.... suggested that this approach works well for certain datasets (i.e. it obtains trees that are close to the model tree) but that the implementation developed by Sankoff and Blanchette, the BPAnalysis software [40] is too slow to be used on anything other than small datasets with a few genes [11, 12]. 6. Breakpoint analysis: Details When each genome has the same set of genes and each gene appears exactly once, a genome can be described by an ordering (circular or linear) of these genes, each gene given with an orientation that is either positive (gi) or negative ( gi) Given two genomes G ....

M. Cosnet, R. Jansen, B. Moret, L. Raubeson, L.-S. Wang, T Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMBOO), pp. 104-115. San Diego, Calif., 2000.

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M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th lnt l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104 115, 2000.

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M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, and S.K. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-

.... phylogenetic trees from gene order data was introduced by Blanchette et al. in [4] It sought to reconstruct the breakpoint phylogeny and was applied to a variety of datasets [5, 28] A different technique for reconstructing phylogenies from gene order data was introduced by Cosner in [8] In [9] we described a simple version of the method, which can also be described as a heuristic for the breakpoint phylogeny, although it is quite different in its technique from BPAnalysis. We call this approach Maximum Parsimony on Binary Encodings (MPBE) The MPBE method first encodes a set of genomes ....

....typical of hill climbing heuristics [21] but will affect the running time proportionally. 2. 4 Our New Method: Maximum Parsimony on Binary Encodings of Genomes (MPBE) In this section we describe a new approach to reconstructing phylogenies from gene order data, which we originally described in [9]. This new method is derived from an earlier method developed by Cosner in [8] Like Cosner s technique, our method encodes the genome data as binary sequences, and seeks a maximum parsimony tree for these sequences. Unlike Cosner s technique, our encoding is very simple and employs no biological ....

[Article contains additional citation context not shown here]

Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., and Wyman, S., "A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data," to appear Proceedings of the 8th Intl. Conf. on Intel. Sys. for Mol. Bio. ISMB'00.

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Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., & Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology ISMB-2000, to appear.

.... suggested that this approach works well for certain datasets (i.e. it obtains trees that are close to the model tree) but that the implementation developed by Sanko# and Blanchette, the BPAnalysis software [30] is too slow to be used on anything other than small datasets with a few genes [9, 10]. 3 Breakpoint Analysis: Details When each genome has the same set of genes and each gene appears exactly once, a genome can be described by an ordering (circular or linear) of these genes, each gene given with an orientation that is either positive (g i ) or negative ( g i ) Given two genomes ....

Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., & Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. Intelligent Systems Mol. Biol. ISMB-2000, San Diego (2000).

....Problem (TSP) for each internal node at each iteration. And hence, the total running time is exponential in both the number of genes and the number of genomes. MPBE. We developed an alternate method, based on a binary encoding of breakpoints, to take advantage of existing parsimony software [9, 10]. This method, called Maximum Parsimony on Binary Encodings (MPBE) is exponential only in the number of genomes (because the parsimony problem is NP hard) runs very fast in practice, but returns only candidate tree topologies and so must make use of the labeling phase of BPAnalysis in order to ....

....it did not eliminate any tree, an expected occurrence when all trees examined have a good topology) The search returned 216 optimal trees, with an inversion score of 67 and a breakpoint score of 84. Since earlier attempts to analyze this dataset found only four trees with an inversion score of 67 [9], this represents a significant advance. 7 High Performance Computing Even the best algorithms for phylogeny reconstruction are likely to take exponential time in many cases, so that we should take advantage of high performance tools whenever possible. We used the best precepts of algorithm ....

[Article contains additional citation context not shown here]

Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., & Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology ISMB2000, San Diego (2000), 104--115.

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M. E. Cosner, R. K. Jansen, B. M. E. Moret, L. A. Raubeson, L.-S. Wang, T. Warnow, and S. K. Wyman, "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes," in Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB00, pp. 104--115, 2000.

....by reversals [2, 12] and a linear time algorithm for computing inversion distances [1] Note that signed permutations correspond to genomes for which the direction of transcription of each gene is known as well as the ordering of the genes. Much recent work on rearrangement based phylogeny [5, 6, 14, 15, 18] stems from an algorithm by Sankoff and Blanchette [17] that iterates over a prospective tree, repeatedly finds medians of the three permutations adjacent to each internal vertex, and uses them to improve the tree until convergence occurs. This method finds locally optimal trees and simultaneously ....

M. Cosner, R. Jansen, B. Moret, L. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology ISMB-2000, pages 104--115, 2000.

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Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., & Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology ISMB-2000, San Diego (2000).

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Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., & Wyman, S., "A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data," Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology ISMB-2000, San Diego (2000).

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Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology ISMB-2000, San Diego, pages 104-115, 2000.

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