Minimum Recombination Histories by Branch and Bound
Recombination plays an important role in creating genetic diversity within species, and inferring past recombination events is central to many problems in genetics. Given a set M of sampled sequences, finding an evolutionary history for M with the minimum number of recombination events is a computationally very challenging problem. In this paper, we present a novel branch and bound algorithm for tackling that problem. Our method is shown to be far more efficient than the only preexisting exact method, described in . Our software implementing the algorithm discussed in this paper is publicly available.
Unable to display preview. Download preview PDF.
- 2.Hudson, R.R., Kaplan, N.L.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147–164 (1985)Google Scholar
- 3.Myers, S.R., Griffiths, R.C.: Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375–394 (2003)Google Scholar
- 4.Gusfield, D., Hickerson, D.: A new lower bound on the number of needed recombination nodes in both unrooted and rooted phylogenetic networks. Technical Report UCD-ECS-06, University of California, Davis (2004)Google Scholar
- 7.Song, Y.S., Wu, Y., Gusfield, D.: Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In: Proceedings of the 13th International Conference on Intelligent Systems for Molecular Biology, ISMB (2005), (in press)Google Scholar
- 9.Griffiths, R.C., Marjoram, P.: An ancestral recombination graph. In: Progress in Population Genetics and Human Evolution. IMA Volumes in Mathematics and its Applications, vol. 87, pp. 257–270. Springer, Heidelberg (1997)Google Scholar
- 10.Kimura, M.: The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61, 893–903 (1969)Google Scholar