K. Atteson, The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction, Algorithmica, vol.25, issue.2-3, pp.251-78, 1999.
DOI : 10.1007/PL00008277

D. Bryant, On the Uniqueness of the Selection Criterion in Neighbor-Joining, Journal of Classification, vol.22, issue.1, pp.3-15, 2005.
DOI : 10.1007/s00357-005-0003-x

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.587-98, 2004.
DOI : 10.1093/molbev/msh049

URL : https://hal.archives-ouvertes.fr/lirmm-00108569

R. Desper and O. Gascuel, The minimum evolution distancebased approach to phylogenetic inference Mathematics of evolution & phylogeny, pp.1-32, 2005.

J. Felsenstein, Inferring phylogenies, 2004.

W. Fitch and E. Margoliash, Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.279-84, 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, Mol Biol Evol, vol.11, pp.961-964, 1994.

O. Gascuel, B. Mirkin, F. Mcmorris, F. Roberts, and A. Rzhetsky, Concerning the NJ algorithm and its unweighted version, UNJ DIMACS series in discrete mathematics and theoretical computer science, Mathematical hierarchies and biology, pp.149-70, 1997.

O. Gascuel, On the Optimization Principle in Phylogenetic Analysis and the Minimum-Evolution Criterion, Molecular Biology and Evolution, vol.17, issue.3, pp.401-406, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026319

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-131, 1980.
DOI : 10.1007/BF01731581

M. Kuhner and J. Felsenstein, A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol Biol Evol, vol.11, pp.459-68, 1994.

S. Kumar, A stepwise algorithm for finding minimum evolution trees, Molecular Biology and Evolution, vol.13, issue.4, pp.584-93, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025618

D. Levy, R. Yoshida, and L. Pachter, Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates, Molecular Biology and Evolution, vol.23, issue.3, 2005.
DOI : 10.1093/molbev/msj059

V. Makarenkov, B. Leclerc, B. Mirkin, F. Mcmorris, F. Roberts et al., Circular orders of tree metrics, and their uses for the reconstruction and fitting of phylogenetic trees Mathematical hierarchies and biology. DIMACS series in discrete mathematics and theoretical computer science, pp.183-208, 1997.

R. Mihaescu, D. Levy, and L. Pachter, Why neighbour-joining works, 2006.

B. Mirkin, Mathematical classification and clustering, 1996.
DOI : 10.1007/978-1-4613-0457-9

M. Nei and S. Kumar, Molecular evolution and phylogenetics, 2000.

M. Nei, S. Kumar, and K. Takahashi, The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small, Proceedings of the National Academy of Sciences, vol.95, issue.21, pp.12390-12397, 1998.
DOI : 10.1073/pnas.95.21.12390

Y. Pauplin, Direct Calculation of a Tree Length Using a Distance Matrix, Journal of Molecular Evolution, vol.51, issue.1, pp.41-48, 2000.
DOI : 10.1007/s002390010065

A. Rzhetsky and M. Nei, Theoretical foundation of the minimumevolution method of phylogenetic inference, Mol Biol Evol, vol.10, pp.1073-95, 1993.

N. Saitou, [25] Reconstruction of gene trees from sequence data, Methods in enzymology, pp.427-476, 1996.
DOI : 10.1016/S0076-6879(96)66027-3

N. Saitou and M. Imanishi, Relative efficiencies of the Fitch- Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic reconstructions in obtaining the correct tree, Mol Biol Evol, vol.6, pp.514-539, 1989.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstruction of phylogenetic trees, Mol Biol Evol, vol.4, pp.406-431, 1987.

C. Semple and M. Steel, Cyclic permutations and evolutionary trees, Advances in Applied Mathematics, vol.32, issue.4, pp.669-80, 2004.
DOI : 10.1016/S0196-8858(03)00098-8

J. Studier and K. Keppler, A note on the neighbor-joining method of Saitou and Nei, Mol Biol Evol, vol.5, pp.729-760, 1998.

K. Sumiyama, C. Kim, and F. Ruddle, An Efficient Cis-Element Discovery Method Using Multiple Sequence Comparisons Based on Evolutionary Relationships, Genomics, vol.71, issue.2, pp.260-262, 2001.
DOI : 10.1006/geno.2000.6422

D. Swofford, G. Olsen, P. Waddell, and D. Hillis, Phylogenetic inference, Molecular sytematics, pp.407-514, 1996.

L. Vinh, V. Haeseler, and A. , 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. Yushmanov, Construction of a tree with p leaves from 2p-3 elements of its distance matrix (Russian), Matematicheskie Zametki, vol.35, pp.877-87, 1984.