K. Atteson, The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction, Algorithmica, vol.25, issue.2-3, pp.251-278, 1999.
DOI : 10.1007/PL00008277

H. J. Bandelt and A. W. Dress, Split decomposition: A new and useful approach to phylogenetic analysis of distance data, Molecular Phylogenetics and Evolution, vol.1, issue.3, pp.242-252, 1992.
DOI : 10.1016/1055-7903(92)90021-8

M. Bordewich, O. Gascuel, K. Huber, and V. 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, issue.1, pp.110-117, 2009.
DOI : 10.1109/TCBB.2008.37
URL : https://hal.archives-ouvertes.fr/lirmm-00324146

M. Bulmer, Use of the method of generalized least squares in reconstructing phylogenies from sequence data, Mol. Biol. Evol, vol.8, issue.6, p.868, 1991.

P. Buneman, The recovery of trees from measures of dissimilarity, Mathematics in the Archaeological and Historical Sciences, pp.387-395, 1971.

L. L. Cavalli-sforza and A. W. Edwards, Analysis of human evolution, Proceedings 11th International Congress of Genetics, pp.923-933, 1964.

L. L. Cavalli-sforza and A. W. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.233-257, 1967.
DOI : 10.2307/2406616

R. Desper and O. Gascuel, Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle, Journal of Computational Biology, vol.9, issue.5, pp.687-705, 2002.
DOI : 10.1089/106652702761034136
URL : https://hal.archives-ouvertes.fr/lirmm-00269513

R. Desper and O. Gascuel, Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting, Molecular Biology and Evolution, vol.21, issue.3, pp.587-598, 2004.
DOI : 10.1093/molbev/msh049
URL : https://hal.archives-ouvertes.fr/lirmm-00108569

R. Desper and O. Gascuel, The minimum evolution distance-based approach to phylogenetic inference, Mathematics of Evolution & Phylogeny, pp.1-32, 2005.

O. Gascuel, On the Optimization Principle in Phylogenetic Analysis and the Minimum-Evolution Criterion, Molecular Biology and Evolution, vol.17, issue.3, pp.401-405, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026319

O. Gascuel and A. Mckenzie, Performance Analysis of Hierarchical Clustering Algorithms, Journal of Classification, vol.21, issue.1, pp.3-18, 2004.
DOI : 10.1007/s00357-004-0003-2
URL : https://hal.archives-ouvertes.fr/lirmm-00108570

O. Gascuel and M. Steel, Neighbor-Joining Revealed, Molecular Biology and Evolution, vol.23, issue.11, 1997.
DOI : 10.1093/molbev/msl072
URL : https://hal.archives-ouvertes.fr/lirmm-00136653

O. Gascuel, D. Bryant, and F. Denis, Strengths and limitations of the minimum evolution principle, Syst. Biol, vol.50, pp.621-627, 2001.

K. K. Kidd and L. A. Sgaramella-zonta, Phylogenetic analysis: concepts and methods, Am. J. Hum. Genet, vol.23, pp.235-252, 1971.

S. Kumar, A stepwise algorithm for finding minimum evolution trees, Molecular Biology and Evolution, vol.13, issue.4, pp.584-593, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025618

R. Mihaescu and L. Pachter, Combinatorics of least-squares trees, Proc. Natl. Acad. Sci. USA 105, pp.13206-13211, 2008.
DOI : 10.1073/pnas.0802089105

M. Nei and S. Kumar, Molecular Evolution and Phylogenetics, 2000.

Y. Pauplin, Direct Calculation of a Tree Length Using a Distance Matrix, Journal of Molecular Evolution, vol.51, issue.1, pp.41-47, 2000.
DOI : 10.1007/s002390010065

A. Rzhetsky and M. Nei, A simple method for estimating and testing minimum-evolution trees, Mol. Biol. Evol, vol.9, pp.945-967, 1992.

A. Rzhetsky and M. Nei, Theoretical foundation of the minimum-evolution method of phylogenetic inference, Mol. Biol. Evol, vol.10, pp.1073-1095, 1993.

N. Saitou and T. Imanishi, Relative efficiencies of the Fitch?Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree, Mol. Biol. Evol, vol.6, pp.514-525, 1989.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, pp.406-425, 1987.

C. Semple and M. Steel, Cyclic permutations and evolutionary trees, Advances in Applied Mathematics, vol.32, issue.4, pp.669-680, 2004.
DOI : 10.1016/S0196-8858(03)00098-8

D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, Phylogenetic inference, Molecular Systematics, pp.407-514, 1996.

L. S. Vinh and A. Von-haeseler, Shortest triplet clustering: reconstructing large phylogenies using representative sets, BMC Bioinformatics, vol.6, issue.1, p.92, 2005.
DOI : 10.1186/1471-2105-6-92

S. J. Willson, Consistent formulas for estimating the total lengths of trees, Discrete Applied Mathematics, vol.148, issue.3, pp.214-239, 2005.
DOI : 10.1016/j.dam.2005.03.005

S. J. Willson, Minimum evolution using ordinary least-squares is less robust than neighbor-joining, Bulletin of Mathematical Biology, vol.67, issue.2, pp.261-279, 2005.
DOI : 10.1016/j.bulm.2004.07.007