M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, S. Wyman, An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae, in: D. Sankoff, J.H. Nadeau (Eds.), Comparative Genomics, Kluwer, Dordrecht, 2000, pp. 99--121.  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... the reversal distance within evolutionary tree reconstruction can be found in [15, 29, 21] For the reasons above, the use of a simpler (though less realistic) notion of distance, called breakpoint distance, which is trivial to compute, has been proposed in [26] and extensively studied afterwards [4, 24, 27, 22, 12, 25, 6]. In particular, much work has been done on the so called Breakpoint Median Problem (BMP) which is the problem of nding a genome which is closest to a given set of genomes w.r.t. the breakpoint distance, i.e. the sum of the breakpoint distances between the genome to be found and each given ....

M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Rauberson, L.-S. Wang, T. Warnow and S. Wyman, \An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae", in [23], 99-121.

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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. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pages 99--122. Kluwer Acad. Pubs., 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. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pages 99--122. Kluwer Academic Press, 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. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pages 99--122. Kluwer Acad. Pubs., 2000.

....an important new source of data for phylogeny reconstruction (see, e.g. 7, 11, 12, 14] 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 symposium [6] was devoted to this topic. A natural optimization problem for phylogeny reconstruction from gene order data is to reconstruct an evolutionary scenario with a minimum number of the permitted evolutionary events on the tree. This problem is NP hard for most criteria even the very simple problem ....

M. Cosner, R. Jansen, B.M.E. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J. Nadeau, editors, Comparative Genomics, pages 99--122. Kluwer Acad. Pubs., 2000.

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Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., 11 & Wyman, S., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families DCAF-

.... 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., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families DCAF-2000, Montreal (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 ....

Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.S., Warnow, T., & Wyman, S., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae, " in Comparative Genomics, D. Sankoff & J.H. Nadeau, eds., Kluwer Acad. Pubs. (2000), 99-- 122.

....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. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J. Nadeau, editors, Comparative Genomics, pages 99--122. Kluwer Academic Press, 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., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families DCAF-2000, Montreal (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., "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae," Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families DCAF-2000, Montreal (2000).

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M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L. Wang, T. Warnow, S. Wyman, An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae, in: D. Sankoff, J.H. Nadeau (Eds.), Comparative Genomics, Kluwer, Dordrecht, 2000, pp. 99--121.

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Cosner, M. E., Jansen, R. K., Moret, B. M. E., Raubeson, L. A., Wang, L.-S., Warnow, T. and Wyman, S. 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. This volume.

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