Inferring Phylogenies.( S i n a u e r ), 2004. ,
Computational molecular evolution.( O x f o r dU n i v e r s i t yP r e s s ), 2006. ,
The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, p.4, 1987. ,
Inferring Phylogenies.( S i n a u e r ), 2004. ,
Toward Extracting All Phylogenetic Information from Matrices of Evolutionary Distances, Science, vol.327, issue.5971, pp.3-7, 2010. ,
DOI : 10.1126/science.1182300
A basic limitation on inferring phylogenies by pairwise sequence comparisons, Journal of Theoretical Biology, vol.256, issue.3, pp.467-472, 2009. ,
DOI : 10.1016/j.jtbi.2008.10.010
Fast and accurate phylogenyr e c o n s t r u c t i o na l g o r i t h m sb a s e do nt h em i n i m u m evolution principle, J. Comp. Biol, vol.96, pp.8-15, 2002. ,
in Molecular Systematics,e d s .H i l l i s, pp.407-514, 1996. ,
Use of the method of generalized least squares in reconstructing phylogenies from sequence data, Mol. Biol. Evol, vol.8, p.8, 1991. ,
Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees, Molecular Biology and Evolution, vol.15, issue.10, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025863
PAUP* ? phylogenetic analysis using parsimony (*and other methods). (Sinauer), 1998. ,
Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.3-3, 1967. ,
DOI : 10.2307/2406616
Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.7-9, 1967. ,
DOI : 10.1126/science.155.3760.279
Phylogenetic analysis: concepts and methods, Am. J. Hum. Genet, vol.23, pp.235-252, 1971. ,
Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximumlikelihood , minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree, Mol. Biol. Evol, vol.65, pp.1-4, 1989. ,
Conceptual and numerical analysis of data,e d .O p i t z ,O .( S p r i n g e r -V e r l a g, pp.2-3, 1989. ,
Theoretical foundation of the minimum-evolution method of phylogenetic inference, Mol. Biol. Evol, vol.10, issue.1, 1993. ,
Theoretical foundation oft h eb a l a n c e dm i n i m u me v o l u t i o nm e t h odo fp h y l o g e n e t i c inference and its relationship to weighted least-squares tree fitting, Mol. Biol. Evol, vol.215, pp.8-15, 2004. ,
Direct Calculation of a Tree Length Using a Distance Matrix, Journal of Molecular Evolution, vol.51, issue.1, pp.1-4, 2000. ,
DOI : 10.1007/s002390010065
Improving the efficiency ofs p rm o v e si np h y l o g e n e t i ct r e es e a r c hm e t h o d sb a s e d on maximum likelihood, Bioinformatics, vol.214, pp.3-3, 2005. ,
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.0-1, 2009. ,
DOI : 10.1109/TCBB.2008.37
URL : https://hal.archives-ouvertes.fr/lirmm-00324146
Combinatorics of least-squares trees, Proc. Natl. Acad. Sci. USA 105, 2008. ,
DOI : 10.1073/pnas.0802089105
Variances of the average numbers ofnucleotidesubstitutionswithinandbetweenpopulations, Mol. Biol. Evol, vol.6, issue.2, 1989. ,
The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction, Algorithmica, vol.25, issue.2-3, pp.251-278, 1999. ,
DOI : 10.1007/PL00008277
Strengths and limitations of the minimum evolution principle, Syst. Biol, vol.506, pp.2-3, 2001. ,
On the consistency of the minimum evolution principle of phylogenetic inference, Discrete Applied Mathematics, vol.127, issue.1, pp.3-7, 2003. ,
DOI : 10.1016/S0166-218X(02)00285-8
URL : https://hal.archives-ouvertes.fr/lirmm-00269579
Consistent formulas for estimating the total lengths of trees, Discrete Applied Mathematics, vol.148, issue.3, pp.1-4, 2005. ,
DOI : 10.1016/j.dam.2005.03.005
Phylogenetics.( O x f o r dU n i v e r s i t yP r e s s ), 2003. ,
Neighbor-Joining Revealed, Molecular Biology and Evolution, vol.23, issue.11, 2006. ,
DOI : 10.1093/molbev/msl072
URL : https://hal.archives-ouvertes.fr/lirmm-00136653
IV.???On Least Squares and Linear Combination of Observations., Proceedings of the Royal Society of Edinburgh, vol.lxiv, pp.42-48, 1935. ,
DOI : 10.1214/aoms/1177732930
Shortest triplet clustering: reconstructing large phylogenies using representative sets, BMC Bioinformatics, vol.69, issue.2, 2005. ,
A c a d e m i cP r e s s ), Mammalian Protein Metabolism, pp.2-3, 1969. ,
A molecular sequence metric and evolutionary trees, Mathematical Biosciences, vol.19, issue.1-2, pp.9-11, 1974. ,
DOI : 10.1016/0025-5564(74)90028-5
On inconsistencyo ft h en e i g h b o r -j o i n i n g ,l e a s ts q u a r e s ,a n dm i n i m u m evolution estimation when substitution processes are incorrectly modeled, Mol. Biol. Evol, vol.21, pp.1-6, 2004. ,
Robustness of Phylogenetic Inference Based on Minimum Evolution, Bulletin of Mathematical Biology, vol.67, issue.2, 2010. ,
DOI : 10.1007/s11538-010-9510-y
URL : https://hal.archives-ouvertes.fr/lirmm-00511779
A simple method for estimating and testing minimum-evolution trees, Mol. Biol. Evol, vol.99, pp.5-9, 1992. ,
A least squares algorithm for fitting additive trees to proximity data, Psychometrika, vol.48, issue.4, pp.621-626, 1983. ,
DOI : 10.1007/BF02293884
Consistent formulas for estimating the total lengths of trees, Discrete Applied Mathematics, vol.148, issue.3, pp.1-4, 2005. ,
DOI : 10.1016/j.dam.2005.03.005
Combinatorics of least-squares trees, Proc. Natl. Acad. Sci. USA 105, pp.13206-13211, 2008. ,
DOI : 10.1073/pnas.0802089105
On the consistency of the minimum evolution principle of phylogenetic inference, Discrete Applied Mathematics, vol.127, issue.1, pp.3-7, 2003. ,
DOI : 10.1016/S0166-218X(02)00285-8
URL : https://hal.archives-ouvertes.fr/lirmm-00269579
Construction of Phylogenetic Trees, Science, vol.155, issue.3760, pp.7-9, 1967. ,
DOI : 10.1126/science.155.3760.279
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.8-15, 2004. ,
DOI : 10.1093/molbev/msh049
URL : https://hal.archives-ouvertes.fr/lirmm-00108569
Direct Calculation of a Tree Length Using a Distance Matrix, Journal of Molecular Evolution, vol.51, issue.1, pp.1-4, 2000. ,
DOI : 10.1007/s002390010065
Strengths and limitations of the minimum evolution principle, Syst. Biol, vol.506, pp.2-3, 2001. ,
Fast and accurate phylogenyr e c o n s t r u c t i o na l g o r i t h m sb a s e do nt h em i n i m u m evolution principle, J. Comp. Biol, vol.96, pp.8-15, 2002. ,