Abstract
The algorithms dealing with the galled tree problem mostly use a conflict graph as the major tool and the construction of the conflict graph has been the central computation in these algorithms. In this paper, we present a parallel algorithm for the construction of a conflict graph. Given a set of n binary sequences, each of size m, our algorithm is mapped on an OTIS-Triangular array and requires 4m + 2n/k –7 electronics moves + 2 OTIS moves, where k = m (m –1)/2. The algorithm is shown to be scalable with respect to n.
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References
Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology. 8, 69–78 (2001)
Myers, S.R., Griffths, R.C.: Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375–394 (2003)
Gusfield, D., Satish, E., Langley, C.: Efficient reconstruction of phylogenetic networks (of SNPs) with constrained recombination. In: Proceedings of 2nd CSB Bioinformatics Conference, Los Alamitos, CA (2003)
Gusfield, D., Satish, E., Langley, C.: Optimal efficient reconstruction of phylogenetic networks with constrained recombination. Journal of Bioinformatics and Computational Biology 2, 173–213 (2004)
Gusfield, D.: Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination, Technical Report, Department of Computer Sc., University of California, Davis, CA
Gusfield, D., Satish, E., Langley, C.: The fine structure of galls in phylogenetic networks. Informs Journal on Computing 16, 459–469 (2004)
Bafna, V., Bansal, V.: The number of recombination events in a sample history conflict graph and lower bounds. IEEE Ttrans. on Computational Biology and Bioinformatics 1, 78–90 (2004)
Marsden, G., Marchand, P., Harvey, P., Esner, S.: Optical transpose interconnection system architectures. Optics Letters 18, 1083–1085 (1993)
Wang, C.-F., Sahni, S.: Matrix Multiplication on the OTIS-Mesh optoelectronic computer. IEEE Transactions on Computers 50(7) (July 2001)
Wang, C.-F., Sahni, S.: Image processing on the OTIS-Mesh optoelectronic Computer. IEEE Transactions on parallel and Distributed Systems 11(2), 97–109 (2000)
Jana, P.K.: Polynomial Interpolation and Polynomial Root Finding on OTIS- Mesh. Parallel Computing 32(4), 301–312 (2006)
Jana, P.K., Sinha, B.P.: An Improved parallel prefix algorithm on OTIS-Mesh. Parallel Processing Letters 16(4), 429–440 (2006)
Wang, C.-F., Sahni, S.: BPC permutations on the OTIS-Mesh optoelectronic computer. In: MPPOI 1997. Proc. of 4th Int’l Conference on Massively Parallel Processing Using Optical Transpose Interconnection, pp. 130–135 (1997)
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Lucas, K.T., Mallick, D.K., Jana, P.K. (2007). Parallel Algorithm for Conflict Graph on OTIS-Triangular Array. In: Rao, S., Chatterjee, M., Jayanti, P., Murthy, C.S.R., Saha, S.K. (eds) Distributed Computing and Networking. ICDCN 2008. Lecture Notes in Computer Science, vol 4904. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77444-0_26
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DOI: https://doi.org/10.1007/978-3-540-77444-0_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77443-3
Online ISBN: 978-3-540-77444-0
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