Abstract
Recently, we have identified a quartet phylogeny algorithm with O(n logn) expected runtime, which is asymptotically optimal. Regardless of the true topology, our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O( loglogn) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of neighbour-joining, which requires O(n 3) runtime. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost.
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References
Brodal, G.S., Fagerberg, R., Pedersen, C.N.S.: Computing the quartet distance between evolutionary trees in time O(n log n). Algorithmica 38(2), 377–395 (2003)
Brown, D.G., Truszkowski, J.: Fast error-tolerant quartet phylogeny algorithms. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 147–161. Springer, Heidelberg (2011)
Bryant, D., Tsang, J., Kearney, P.E., Li, M.: Computing the quartet distance between evolutionary trees. In: Proceedings of SODA 2000, pp. 285–286 (2000)
Csűrös, M.: Fast recovery of evolutionary trees with thousands of nodes. J. Comp. Biol. 9(2), 277–297 (2002)
Daskalakis, C., Mossel, E., Roch, S.: Phylogenies without branch bounds: Contracting the short, pruning the deep. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 451–465. Springer, Heidelberg (2009)
Desper, R., Gascuel, O.: Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comp. Biol. 9(5), 687–706 (2002)
Elias, I., Lagergren, J.: Fast neighbor joining. In: Caires, L., Italiano, G.F., Monteiro, L., Palamidessi, C., Yung, M. (eds.) ICALP 2005. LNCS, vol. 3580, pp. 1263–1274. Springer, Heidelberg (2005)
Erdös, P.L., Steel, M.A., Székely, L.A., Warnow, T.: A few logs suffice to build (almost) all trees: Part II. Theor. Comput. Sci. 221(1-2), 77–118 (1999)
Gronau, I., Moran, S.: Optimal implementations of UPGMA and other common clustering algorithms. Inf. Process. Lett. 104(6), 205–210 (2007)
Kannan, S.K., Lawler, E.L., Warnow, T.J.: Determining the evolutionary tree using experiments. J. Algorithms 21(1), 26–50 (1996)
Karp, R.M., Kleinberg, R.: Noisy binary search and its applications. In: Proceedings of SODA 2007, pp. 881–890 (2007)
Kearney, P.E.: The ordinal quartet method. In: Proceedings of RECOMB 1998, pp. 125–134 (1998)
King, V., Zhang, L., Zhou, Y.: On the complexity of distance-based evolutionary tree reconstruction. In: Proceedings of SODA 2003, pp. 444–453 (2003)
Price, M.N., Dehal, P.S., Arkin, A.P.: FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26(7), 1641–1650 (2009)
Ranwez, V., Gascuel, O.: Quartet-based phylogenetic inference: Improvements and limits. Mol. Biol. Evol. 18(6), 1103–1116 (2001)
Snir, S., Warnow, T., Rao, S.: Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm. J. Comp. Biol. 15(1), 91–103 (2008)
Sonnhammer, E.L.L., Hollich, V.: Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinf. 6, 108 (2005)
Strimmer, K., Goldman, N., von Haeseler, A.: Bayesian probabilities and quartet puzzling. Mol. Biol. Evol. 14(2), 210–211 (1996)
Strimmer, K., von Haeseler, A.: Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13(7), 964–969 (1996)
Wheeler, T.J.: Large-scale neighbor-joining with NINJA. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 375–389. Springer, Heidelberg (2009)
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Brown, D.G., Truszkowski, J. (2011). Towards a Practical O(n logn) Phylogeny Algorithm. In: Przytycka, T.M., Sagot, MF. (eds) Algorithms in Bioinformatics. WABI 2011. Lecture Notes in Computer Science(), vol 6833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23038-7_2
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DOI: https://doi.org/10.1007/978-3-642-23038-7_2
Publisher Name: Springer, Berlin, Heidelberg
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