Abstract
The rooted triplet distance measures the structural dissimilarity of two phylogenetic trees or networks by counting the number of rooted trees with exactly three leaf labels that occur as embedded subtrees in one, but not both of them. Suppose that \(N_1 = (V_1, E_1)\) and \(N_2 = (V_2, E_2)\) are rooted phylogenetic networks over a common leaf label set of size \(\lambda \), that \(N_i\) has level \(k_i\) and maximum in-degree \(d_i\) for \(i \in \{1,2\}\), and that the networks’ out-degrees are unbounded. Denote \(n = \max (|V_1|, |V_2|)\), \(m = \max (|E_1|, |E_2|)\), \(k = \max (k_1, k_2)\), and \(d = \max (d_1, d_2)\). Previous work has shown how to compute the rooted triplet distance between \(N_1\) and \(N_2\) in \(\mathrm {O}(\lambda \log \lambda )\) time in the special case \(k \le 1\). For \(k > 1\), no efficient algorithms are known; a trivial approach leads to a running time of \(\mathrm {\Omega }(n^{7} \lambda ^{3})\) and the only existing non-trivial algorithm imposes restrictions on the networks’ in- and out-degrees (in particular, it does not work when non-binary nodes are allowed). In this paper, we develop two new algorithms that have no such restrictions. Their running times are \(\mathrm {O}(n^{2} m + \lambda ^{3})\) and \(\mathrm {O}(m + k^{3} d^{3} \lambda + \lambda ^{3})\), respectively. We also provide implementations of our algorithms and evaluate their performance in practice. This is the first publicly available software for computing the rooted triplet distance between unrestricted networks of arbitrary levels.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Brodal, G.S., Mampentzidis, K.: Cache oblivious algorithms for computing the triplet distance between trees. In: Proceedings of ESA 2017, pp. 21:1–21:14 (2017)
Byrka, J., Gawrychowski, P., Huber, K.T., Kelk, S.: Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. J. Discrete Algorithms 8(1), 65–75 (2010)
Cardona, G., Rosselló, F., Valiente, G.: Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinform. 9(1), 532 (2008)
Choy, C., Jansson, J., Sadakane, K., Sung, W.K.: Computing the maximum agreement of phylogenetic networks. Theor. Comput. Sci. 335(1), 93–107 (2005)
Dobson, A.J.: Comparing the shapes of trees. In: Street, A.P., Wallis, W.D. (eds.) Combinatorial Mathematics III. Lecture Notes in Mathematics, vol. 452, pp. 95–100. Springer, Berlin (1975). https://doi.org/10.1007/BFb0069548
Estabrook, G., McMorris, F., Meacham, C.: Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34(2), 193–200 (1985)
Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc., Sunderland (2004)
Fortune, S., Hopcroft, J., Wyllie, J.: The directed subgraph homeomorphism problem. Theor. Comput. Sci. 10(2), 111–121 (1980)
Francis, A.R., Steel, M.: Which phylogenetic networks are merely trees with additional arcs? Syst. Biol. 64(5), 768–777 (2015)
Gambette, P., Huber, K.T.: On encodings of phylogenetic networks of bounded level. J. Math. Biol. 65(1), 157–180 (2012)
Gusfield, D., Eddhu, S., Langley, C.: Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol. 2(1), 173–213 (2004)
Jansson, J., Lingas, A.: Computing the rooted triplet distance between galled trees by counting triangles. J. Discrete Algorithms 25, 66–78 (2014)
Jansson, J., Rajaby, R., Sung, W.K.: An efficient algorithm for the rooted triplet distance between galled trees. In: Proceedings of AlCoB 2017, pp. 115–126 (2017)
Jetten, L., van Iersel, L.: Nonbinary tree-based phylogenetic networks. IEEE/ACM Trans. Comput. Biol. Bioinform. 1(1), 205–217 (2018)
Marcussen, T., Heier, L., Brysting, A.K., Oxelman, B., Jakobsen, K.S.: From gene trees to a dated allopolyploid network: insights from the angiosperm genus viola (violaceae). Syst. Biol. 64(1), 84–101 (2015)
McKenzie, A., Steel, M.: Distributions of cherries for two models of trees. Math. Biosci. 164(1), 81–92 (2000)
Robinson, D., Foulds, L.: Comparison of phylogenetic trees. Math. Biosci. 53(1), 131–147 (1981)
Shiloach, Y., Perl, Y.: Finding two disjoint paths between two pairs of vertices in a graph. J. ACM 25(1), 1–9 (1978)
Acknowledgments
Konstantinos Mampentzidis acknowledges the support by the Danish National Research Foundation, grant DNRF84, via the Center for Massive Data Algorithmics (MADALGO).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Jansson, J., Mampentzidis, K., Rajaby, R., Sung, WK. (2019). Computing the Rooted Triplet Distance Between Phylogenetic Networks. In: Colbourn, C., Grossi, R., Pisanti, N. (eds) Combinatorial Algorithms. IWOCA 2019. Lecture Notes in Computer Science(), vol 11638. Springer, Cham. https://doi.org/10.1007/978-3-030-25005-8_24
Download citation
DOI: https://doi.org/10.1007/978-3-030-25005-8_24
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-25004-1
Online ISBN: 978-3-030-25005-8
eBook Packages: Computer ScienceComputer Science (R0)