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Matching Split Distance for Unrooted Binary Phylogenetic Trees
January/February 2012 (vol. 9 no. 1)
pp. 150-160
D. Bogdanowicz, Dept. of Algorithms & Syst. Modeling, Gdansk Univ. of Technol., Gdansk, Poland
K. Giaro, Dept. of Algorithms & Syst. Modeling, Gdansk Univ. of Technol., Gdansk, Poland
The reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents the historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we propose a new method of defining distances between unrooted binary phylogenetic trees that is especially useful for relatively large phylogenetic trees. Next, we investigate in detail the properties of one example of these metrics, called the Matching Split distance, and describe how the general method can be extended to nonbinary trees.

[1] B.L. Allen and M. Steel, “Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees,” Annals of Combinatorics, vol. 5, pp. 1-15, 2001.
[2] J. Bluis and D.-G. Shin, “Nodal Distance Algorithm: Calculating a Phylogenetic Tree Comparison Metric,” Proc. Third IEEE Symp. BioInformatics and BioEng., pp. 87-94, 2003.
[3] D. Bogdanowicz, “Analyzing Sets of Phylogenetic Trees Using Metrics,” Applicationes Mathematicae, vol. 38, no. 1, pp. 1-16, 2011.
[4] D. Bryant, “The Splits in the Neighborhood Tree,” Annals of Combinatorics, vol. 8, pp. 1-11, 2004.
[5] D. Bryant, “Building Trees, Hunting for Trees, and Comparing Trees Theory and Methods in Phylogenetic Analysis,” PhD thesis, Dept. of Math., Univ. of Canterbury, 1997.
[6] B. Dasgupta, X. He, T. Jiang, M. Li, J. Tromp, and L. Zhang, “On Distances between Phylogenetic Trees,” Proc. Eighth Ann. ACM-SIAM Symp. Discrete Algorithms (SODA), pp. 427-436, 1997.
[7] G.F. Estabrook, F.R. McMorris, and C.A. Meacham, “Comparison of Undirected Phylogenetic Trees Based on Subtrees of 4 Evolutionary Units,” Systematic Biology, vol. 34, pp. 193-200, 1985.
[8] J. Felsenstein, Inferring Phylogenies. Sinauer Assoc. 2003.
[9] H.N. Gabow and R.E. Tarjan, “Faster Scaling Algorithms for Network Problems,” SIAM J. Computing, vol. 18, pp. 1013-1036, 1989.
[10] D. Gusfield, “Efficient Algorithms for Inferring Evolutionary Trees,” Networks, vol. 21, pp. 19-28, 1991.
[11] G. Hickey, F. Dehne, A. Rau-Chaplin, and C. Blouin, “SPR Distance Computation for Unrooted Trees,” Evolutionary Bioinformatics, vol. 4, pp. 17-27, 2008.
[12] D.M. Hillis, T.A. Heath, and K.S. John, “Analysis and Visualization of Tree Space,” Systematic Biology, vol. 54, no. 3, pp. 471-482, 2005.
[13] M. Li, J. Tromp, and L. Zhang, “On the Nearest Neighbour Interchange Distance between Evolutionary Trees,” J. Theoretical Biology, vol. 182, no. 4, pp. 463-467, 1996.
[14] A. McKenzie and M. Steel, “Distributions of Cherries for Two Models of Trees,” Math. Biosciences, vol. 164, no. 1, pp. 81-92, 2000.
[15] T. Munzner, F. Guimbretière, S. Tasiran, L. Zhang, and Y. Zhou, “TreeJuxtaposer: Scalable Tree Comparison Using Focus+Context with Guaranteed Visibility,” ACM Trans. Graphics, vol. 22, no. 3, pp. 453-462, 2003.
[16] J.B. Orlin and R.K. Ahuja, “New Scaling Algorithms for the Assignment and Minimum Mean Cycle Problems,” Math. Programming, vol. 54, pp. 41-56, 1992.
[17] D.F. Robinson and L.R. Foulds, “Comparison of Phylogenetic Trees,” Math. Biosciences, vol. 53, pp. 131-147, 1981.
[18] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[19] M.A. Steel and D. Penny, “Distributions of Tree Comparison Metrics - Some New Results,” Systematic Biology, vol. 42, no. 2, pp. 126-141, 1993.
[20] C. Stockham, L.-S. Wang, and T. Warnow, “Statistically Based Postprocessing of Phylogenetic Analysis by Clustering,” Bioinformatics, vol. 18, no. suppl. 1, pp. S285-S293, 2002.
[21] D.M. de Vienne, T. Giraud, and O.C. Martin, “A Congruence Index for Testing Topological Similarity between Trees,” Bioinformatics, vol. 23, pp. 3119-3124, 2007.
[22] J.T.L. Wang, H. Shan, D. Shasha, and W.H. Piel, “Fast Structural Search in Phylogenetic Databases,” Evolutionary Bioinformatics, vol. 1, pp. 37-46, 2005.

Index Terms:
trees (mathematics),evolution (biological),genetics,evolutionary tree reconstruction,matching split distance,unrooted binary phylogenetic trees,Measurement,Phylogeny,Bipartite graph,Artificial neural networks,Radio frequency,Bioinformatics,Computational biology,matching split distance.,Phylogenetic tree,phylogenetic tree metric,phylogenetic tree comparison,splits,minimum-weight perfect matching
D. Bogdanowicz, K. Giaro, "Matching Split Distance for Unrooted Binary Phylogenetic Trees," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 1, pp. 150-160, Jan.-Feb. 2012, doi:10.1109/TCBB.2011.48
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