R. Agarwala, V. Bafna, M. Farach, M. Paterson, and M. Thorup, On the Approximability of Numerical Taxonomy (Fitting Distances by Tree Metrics), SIAM Journal on Computing, vol.28, issue.3, pp.1073-1085, 1999.
DOI : 10.1137/S0097539795296334

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

H. Bandelt and A. 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

J. Barthélemy and A. Guénoche, Trees and Proximity Representations, 1991.

W. J. Bruno, N. D. Socci, and A. L. Halpern, Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction, Molecular Biology and Evolution, vol.17, issue.1, pp.189-197, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026231

D. Bryant and P. Waddell, Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees, Molecular Biology and Evolution, vol.15, issue.10, pp.1346-1359, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025863

M. Bulmer, Use of the method of generalized least squares in reconstructing phylogenies from sequence data, Molecular Biology and Evolution, vol.8, pp.868-883, 1991.

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

L. Cavalli-sforza and A. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.550-570, 1967.
DOI : 10.2307/2406616

W. H. Day, Computational complexity of inferring phylogenies from dissimilarity matrices, Bulletin of Mathematical Biology, vol.42, issue.4, pp.461-467, 1987.
DOI : 10.1007/BF02458863

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 M. Vingron, Tree Fitting: Topological Recognition from Ordinary Least-Squares Edge Length Estimates, Journal of Classification, vol.19, issue.1, pp.87-112, 2002.
DOI : 10.1007/s00357-001-0034-x

M. Farach, S. Kannan, and T. Warnow, A robust model for finding optimal evolutionary trees, Algorithmica, vol.2, issue.1, pp.155-179, 1995.
DOI : 10.1007/BF01188585

J. Felsenstein, Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters, Systematic Zoology, vol.22, issue.3, pp.240-249, 1978.
DOI : 10.2307/2412304

J. Felsenstein, Distance Methods for Inferring Phylogenies: A Justification, Evolution, vol.38, issue.1, pp.16-24, 1984.
DOI : 10.2307/2408542

J. Felsenstein, An Alternating Least Squares Approach to Inferring Phylogenies from Pairwise Distances, Systematic Biology, vol.46, issue.1, pp.101-111, 1997.
DOI : 10.1093/sysbio/46.1.101

W. M. Fitch and E. Margoliash, Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.279-284, 1967.
DOI : 10.1126/science.155.3760.279

O. Gascuel, A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances, Molecular Biology and Evolution, vol.11, pp.961-961, 1994.

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

O. Gascuel, Concerning the NJ algorithm and its unweighted version, UNJ. In Mathematical Hierarchies and Biology, pp.149-170, 1997.

O. Gascuel, Data Model and Classification by Trees: The Minimum Variance Reduction (MVR) Method, Journal of Classification, vol.17, issue.1, pp.67-69, 2000.
DOI : 10.1007/s003570000005

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, D. Bryant, D. , and F. , Strengths and limitations of the minimum evolution principle, Systematic Biology, vol.50, issue.5, pp.621-627, 2001.

O. Gascuel and D. Levy, A reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance, Journal of Classification, vol.20, issue.1, pp.129-155, 1996.
DOI : 10.1007/BF01202585

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

E. F. Harding, The Probabilities of Rooted Tree-Shapes Generated by Random Bifurcation, Advances in Applied Probability, vol.3, issue.1, pp.44-77, 1971.
DOI : 10.2307/1426329

L. J. Hubert and P. Arabie, Iterative projection strategies for the least-squares fitting of tree structures to proximity data, British Journal of Mathematical and Statistical Psychology, vol.48, issue.2, pp.281-317, 1995.
DOI : 10.1111/j.2044-8317.1995.tb01065.x

T. H. Jukes and C. R. Cantor, Evolution of Protein Molecules, pp.21-132, 1969.
DOI : 10.1016/B978-1-4832-3211-9.50009-7

K. K. Kidd and L. A. Sgaramella-zonta, Phylogenetic analysis: Concepts and methods, American Journal of Human Genetics, vol.23, pp.235-252, 1971.

M. K. Kuhner and J. Felsenstein, A simulation comparison of phylogeny algorithms under equal and unequal rates, Molecular Biology and Evolution, vol.11, issue.3, pp.459-468, 1994.

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

C. M. Lawson and R. J. Hanson, Solving Least Squares Problems, 1974.
DOI : 10.1137/1.9781611971217

V. Makarenkov and B. Leclerc, An Algorithm for the Fitting of a Tree Metric According to a Weighted Least-Squares Criterion, Journal of Classification, vol.16, issue.1, pp.3-26, 1999.
DOI : 10.1007/s003579900040

M. Nei and L. Jin, Variances of the average numbers of nucleotide substitutions within and between populations, Molecular Biology and Evolution, vol.6, pp.290-300, 1989.

M. Nei, J. C. Stephens, and N. Saitou, Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular date from humans and apes, Molecular Biology and Evolution, vol.2, issue.1, pp.66-85, 1985.

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, Theoretical foundation of the minimumevolution method of phylogenetic inference, Molecular Biology and Evolution, vol.10, issue.5, pp.1073-1095, 1993.

N. Saitou and M. Nei, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, vol.4, issue.4, pp.406-425, 1987.

M. J. Sanderson, M. J. Donoghue, W. Piel, and T. Eriksson, Tree- BASE: A prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life, American Journal of Botany, issue.6, pp.81-183, 1994.

S. Sattath and A. Tversky, Additive similarity trees, Psychometrika, vol.42, issue.3, pp.319-345, 1977.
DOI : 10.1007/BF02293654

C. Semple and M. Steel, Phylogenetics, 2003.

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

P. H. Sneath and R. R. Sokal, Numerical Taxonomy, W.K. Freeman and Company, vol.46, pp.230-234, 1973.
DOI : 10.1002/9781118960608.bm00018

J. A. Studier and K. J. Keppler, A note on the neighbor-joining algorithm of Saitou and Nei, Molecular Biology and Evolution, vol.5, issue.6, pp.729-731, 1988.

E. Susko, Confidence Regions and Hypothesis Tests for Topologies Using Generalized Least Squares, Molecular Biology and Evolution, vol.20, issue.6, pp.862-868, 2003.
DOI : 10.1093/molbev/msg093

D. Swofford, PAUP?Phylogenetic Analysis Using Parsimony (and other methods), 1996.

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

W. Vach, Least squares approximation of addititve trees, Conceptual and Numerical Analysis of Data, pp.230-238, 1989.

G. U. Yule, A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S., Philosophical Transactions of the Royal Society B: Biological Sciences, vol.213, issue.402-410, pp.21-87, 1925.
DOI : 10.1098/rstb.1925.0002

K. Zaretskii, Constructing a tree on the basis of a set of distances between the hanging vertices, Russian, Uspeh Mathematicheskikh Nauk, pp.90-92, 1965.