Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

Magnus Bordewich1, Olivier Gascuel2, Katharina T. Huber3, Vincent Moulton3
1[Dept. of Comput. Sci., Univ. of Durham, Durham]
2Methodes et Algorithmes pour la Bioinformatique, LIRMM, Montpellier
3Sch. of Comput. Sci., Univ. of East Anglia, Norwich

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Allen, 2001, Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees, Annals of Combinatorics, 5, 1, 10.1007/s00026-001-8006-8

Atteson, 1999, The Performance of the Neighbor-Joining Methods of Phylogenetic Reconstruction, Algorithmica, 25, 251, 10.1007/PL00008277

Bruno, 2000, Weighted Neighbor Joining: A Likelihood Based Approach to Distance-Based Phylogeny Reconstruction, Molecular Biology and Evolution, 17, 189, 10.1093/oxfordjournals.molbev.a026231

Bryant, 2004, The Splits in the Neighbourhood of a Tree, Annals of Combinatorics, 8, 1, 10.1007/s00026-004-0200-z

Bryant, Computing the Quartet Distance between Evolutionary Trees, Proc. 11th Ann. ACM-SIAM Symp. Discrete Algorithms (SODA ’00), 285

Desper, 2002, Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum Evolution Principle, J. Computational Biology, 9, 587

Desper, 2004, Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting, Molecular Biology and Evolution, 21, 587, 10.1093/molbev/msh049

Desper, 2005, The Minimum-Evolution Distance Based Approach to Phylogenetic Inference, Math. Evolution and Phylogeny, 10.1093/oso/9780198566106.003.0001

Desper, 2008, Distance-Based Phylogeny Reconstruction, (Optimal Radius; 1999, Atteson2005, Elias and Lagergren), Encyclopedia of Algorithms, 1, 10.1007/978-0-387-30162-4_115

Estabrook, 1985, Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units, Systematic Zoology, 34, 192, 10.2307/2413326

Felsenstein, 1989, PHYLIP—Phylogeny Inference Package (Version 3.2), Cladistics, 5, 164

Felsenstein, 1997, An Alternating Least-Squares Approach to Inferring Phylogenies from Pairwise Distances, Systematic Biology, 46, 101, 10.1093/sysbio/46.1.101

Felsenstein, 2004, Inferring Phylogenies

Gascuel, 1997, BIONJ: An Improved Version of the NJ Algorithm Based on a Simple Model of Sequence Data, Molecular Biology and Evolution, 14, 685, 10.1093/oxfordjournals.molbev.a025808

Gascuel, 2005, Sur la Consistance et le Rayon de Sécurité du Principe d’Évolution Minimum, internal report in French (available on request)

Hordijk, 2005, Improving the Efficiency of SPR Moves in Phylogenetic Tree Search Methods Based on Maximum Likelihood, Bioinformatics, 21, 4338, 10.1093/bioinformatics/bti713

Kidd, 1971, Phylogenetic Analysis: Concepts and Methods, Am. J. Human Genetics, 23, 235

Mailund, 2004, QDist—Quartet Distance between Evolutionary Trees, Bioinformatics, 20, 1363, 10.1093/bioinformatics/bth097

Pauplin, 2000, Direct Calculation of Tree Length Using a Distance Matrix, J. Molecular Evolution, 51, 66, 10.1007/s002390010065

Rzhetsky, 1993, Theoretical Foundation of the Minimum-Evolution Method of Phylogenetic Inference, Molecular Biology and Evolution, 10, 1073

Robinson, 1981, Comparison of Phylogenetic Trees, Math. Biosciences, 53, 131, 10.1016/0025-5564(81)90043-2

Saitou, 1987, The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees, Molecular Biology and Evolution, 4, 406

Sneath, 1973, Numerical Taxonomy, 230

Semple, 2003, Phylogenetics, 10.1093/oso/9780198509424.001.0001

Semple, 2004, Cyclic Permutations and Evolutionary Trees, Advances in Applied Math., 32, 669, 10.1016/S0196-8858(03)00098-8

Steel, 1993, Distributions of Tree Comparison Metrics—Some New Results, Systematic Biology, 42, 126

Strimmer, 1996, Quartet Puzzling: A Quartet Maximum Likelihood Method for Reconstructing Tree Topologies, Molecular Biology and Evolution, 13, 964, 10.1093/oxfordjournals.molbev.a025664

Swofford, 2003, PAUP*, Phylogenetic Analysis Using Parsimony (∗ and Other Methods)

Vinh, 2005, Shortest Triplet Clustering: Reconstructing Large Phylogenies Using Representative Sets, BMC Bioinformatics, 6, 1

Willson, 2005, Minimum Evolution Using Ordinary Least Squares Is Less Robust Than Neighbor-Joining, Bull. Math. Biology, 67, 261, 10.1016/j.bulm.2004.07.007