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Magnus Bordewich, Olivier Gascuel, Katharina T. Huber, Vincent Moulton, "Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 110117, JanuaryMarch, 2009.  
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@article{ 10.1109/TCBB.2008.37, author = {Magnus Bordewich and Olivier Gascuel and Katharina T. Huber and Vincent Moulton}, title = {Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {6}, number = {1}, issn = {15455963}, year = {2009}, pages = {110117}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.37}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference IS  1 SN  15455963 SP110 EP117 EPD  110117 A1  Magnus Bordewich, A1  Olivier Gascuel, A1  Katharina T. Huber, A1  Vincent Moulton, PY  2009 KW  phylogenetic tree KW  subtree prune and regraft (SPR) KW  BSPR algorithm KW  Nearest Neighbor Interchange (NNI) KW  BNNI algorithm KW  balanced minimum evolution principle (BME) KW  treelength KW  quartetdistance KW  Robinson Foulds distance KW  consistency KW  safety radius KW  topological move VL  6 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] B. Allen and M. Steel, “Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees,” Annals of Combinatorics, vol. 5, pp. 113, 2001.
[2] K. Atteson, “The Performance of the NeighborJoining Methods of Phylogenetic Reconstruction,” Algorithmica, vol. 25, pp. 251278, 1999.
[3] W.J. Bruno, N.D. Socci, and A.L. Halpern, “Weighted Neighbor Joining: A Likelihood Based Approach to DistanceBased Phylogeny Reconstruction,” Molecular Biology and Evolution, vol. 17, pp.189197, 2000.
[4] D. Bryant, “The Splits in the Neighbourhood of a Tree,” Annals of Combinatorics, vol. 8, pp. 111, 2004.
[5] D. Bryant, J. Tsang, P.E. Kearney, and M. Li, “Computing the Quartet Distance between Evolutionary Trees,” Proc. 11th Ann. ACMSIAM Symp. Discrete Algorithms (SODA '00), pp. 285286, Jan. 2000.
[6] R. Desper and O. Gascuel, “Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum Evolution Principle,” J. Computational Biology, vol. 9, pp. 587598, http://atgc.lirmm.frfastme/, 2002.
[7] R. Desper and O. Gascuel, “Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted LeastSquares Tree Fitting,” Molecular Biology and Evolution, vol. 21, pp. 587598, 2004.
[8] R. Desper and O. Gascuel, “The MinimumEvolution Distance Based Approach to Phylogenetic Inference,” Math. Evolution and Phylogeny, O. Gascuel, ed. Oxford Univ. Press, 2005.
[9] R. Desper and O. Gascuel, “DistanceBased Phylogeny Reconstruction, (Optimal Radius; 1999, Atteson2005, Elias and Lagergren),” Encyclopedia of Algorithms, M.Y. Kao, ed., chapter, pp.199, Springer, 2008.
[10] R. Desper, V. Lefort, H. Phan, and O. Gascuel, manuscript in preparation.
[11] G.F. Estabrook, F.R. McMorris, and C.A. Meacham, “Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units,” Systematic Zoology, vol. 34, pp. 192200, 1985.
[12] J. Felsenstein, “PHYLIP—Phylogeny Inference Package (Version3.2),” Cladistics, vol. 5, pp. 164166, 1989.
[13] J. Felsenstein, “An Alternating LeastSquares Approach to Inferring Phylogenies from Pairwise Distances,” Systematic Biology, vol. 46, pp. 101111, 1997.
[14] J. Felsenstein, Inferring Phylogenies. Sinauer Assoc., Inc., 2004.
[15] O. Gascuel, “BIONJ: An Improved Version of the NJ Algorithm Based on a Simple Model of Sequence Data,” Molecular Biology and Evolution, vol. 14, pp. 685695, 1997.
[16] O. Gascuel and S. Guillemot, “Sur la Consistance et le Rayon de Sécurité du Principe d'Évolution Minimum,” internal report in French (available on request), 2005
[17] W. Hordijk and O. Gascuel, “Improving the Efficiency of SPR Moves in Phylogenetic Tree Search Methods Based on Maximum Likelihood,” Bioinformatics, vol. 21, no. 24, pp. 43384347, 2005.
[18] K.K. Kidd and L.A. SgaramellaZonta, “Phylogenetic Analysis: Concepts and Methods,” Am. J. Human Genetics, vol. 23, pp.235252, 1971.
[19] T. Mailund and C.N.S. Pedersen, “QDist—Quartet Distance between Evolutionary Trees,” Bioinformatics, vol. 20, no. 10, pp.13631637, 2004.
[20] Y. Pauplin, “Direct Calculation of Tree Length Using a Distance Matrix,” J. Molecular Evolution, vol. 51, pp. 6685, 2000.
[21] A. Rzhetsky and M. Nei, “Theoretical Foundation of the MinimumEvolution Method of Phylogenetic Inference,” Molecular Biology and Evolution, vol. 10, pp. 10731095, 1993.
[22] D. Robinson and L. Foulds, “Comparison of Phylogenetic Trees,” Math. Biosciences, vol. 53, pp. 131147, 1981.
[23] N. Saitou and M. Nei, “The NeighborJoining Method: A New Method for Reconstructing Phylogenetic Trees,” Molecular Biology and Evolution, vol. 4, pp. 406424, 1987.
[24] P.H.A Sneath and R.R. Sokal, Numerical Taxonomy, pp. 230234. W.K. Freeman, 1973.
[25] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[26] C. Semple and M. Steel, “Cyclic Permutations and Evolutionary Trees,” Advances in Applied Math., vol. 32, pp. 669680, 2004.
[27] M. Steel and D. Penny, “Distributions of Tree Comparison Metrics—Some New Results,” Systematic Biology, vol. 42, no. 2, pp. 126141, 1993.
[28] K. Strimmer and A. von Haeseler, “Quartet Puzzling: A Quartet Maximum Likelihood Method for Reconstructing Tree Topologies,” Molecular Biology and Evolution, vol. 13, pp. 964969, 1996.
[29] D.L. Swofford, ${\rm PAUP}^{\ast}$ , Phylogenetic Analysis Using Parsimony ($^{\ast}$ and Other Methods). Sinauer Assoc., Inc., 2003.
[30] L.S. Vinh and A. von Haeseler, “Shortest Triplet Clustering: Reconstructing Large Phylogenies Using Representative Sets,” BMC Bioinformatics, vol. 6, no. 92, pp. 114, 2005.
[31] S.J. Willson, “Minimum Evolution Using Ordinary Least Squares Is Less Robust Than NeighborJoining,” Bull. Math. Biology, vol. 67, pp. 261279, 2005.