Abstract
Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by Ma et al. (2008a) in the context of reconstructing evolutionary histories of genomes in the infinite sites model. In this paper, we show that the original algorithm by Ma et al. (2008a) is incorrect, and we propose a modified algorithm that addresses the problems that we discovered. Moreover, by adapting a data structure by Amir et al. (2007), we were able to improve the running time from O(mn) to \(O(n+m\log m)\), where n is the size of the species tree, and m is the size of the gene tree.
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References
Amir, A., Landau, G.M., Lewenstein, M., Sokol, D.: Dynamic text and static pattern matching. ACM Trans. Algorithms 3(2), 19 (2007)
Bansal, M.S., Alm, E.J., Kellis, M.: Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28(12), i283–i291 (2012)
Bender, M.A., Farach-Colton, M.: The LCA problem revisited. In: Gonnet, Gaston H., Viola, Alfredo (eds.) LATIN 2000. LNCS, vol. 1776, pp. 88–94. Springer, Heidelberg (2000)
Berkman, O., Vishkin, U.: Finding level-ancestors in trees. J. Comput. Syst. Sci. 48(2), 214–230 (1994)
Doyon, J.-P., Hamel, S., Chauve, C.: An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework. IEEE/ACM Trans. Comput. Biol. Bioinform. 9(1), 26–39 (2012)
Doyon, J.-P., Scornavacca, C., Gorbunov, K.Y., Szöllősi, G.J., Ranwez, V., Berry, V.: An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 93–108. Springer, Heidelberg (2010)
Eulenstein, O.: A linear time algorithm for tree mapping. GMD-Forschungszentrum Informationstechnik (1997)
Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Sunderland (2004)
Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press, Cambridge (2009)
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Biol. 28(2), 132–163 (1979)
Górecki, P., Burleigh, G.J., Eulenstein, O.: Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinform. 12(1), 1 (2011)
Guigo, R., Muchnik, I., Smith, T.F.: Reconstruction of ancient molecular phylogeny. Mol. Phylogenet. Evol. 6(2), 189–213 (1996)
Harel, D., Tarjan, R.E.: Fast algorithms for finding nearest common ancestors. SIAM J. Comput. 13(2), 338–355 (1984)
Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Miller, W., Haussler, D.: The infinite sites model of genome evolution. Proc. Nat. Acad. Sci. 105(38), 14254–14261 (2008a)
Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Zhang, L., Miller, W., Haussler, D.: DUPCAR: reconstructing contiguous ancestral regions with duplications. J. Comput. Biol. 15(8), 1007–1027 (2008b)
Sennblad, B., Lagergren, J.: Probabilistic orthology analysis. Syst. Biol. 58(4), 411–424 (2009)
Zhang, L.: On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comput. Biol. 4(2), 177–187 (1997)
Zmasek, C.M., Eddy, S.R.: A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17(9), 821–828 (2001)
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This research was funded by a grant from the Slovak Research and Development Agency APVV-14-0253 and by VEGA grants 1/0684/16, 1/0719/14, and 2/0165/16.
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Brejová, B., Gafurov, A., Pardubská, D., Sabo, M., Vinař, T. (2016). Isometric Gene Tree Reconciliation Revisited. In: Frith, M., Storm Pedersen, C. (eds) Algorithms in Bioinformatics. WABI 2016. Lecture Notes in Computer Science(), vol 9838. Springer, Cham. https://doi.org/10.1007/978-3-319-43681-4_4
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DOI: https://doi.org/10.1007/978-3-319-43681-4_4
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