J. P. Benzecri, Sur le calcul des taux d'inertie dans l'analyse d'un questionnaire, pp.377-378, 1979.

P. Buchy, S. Mardy, S. Vong, T. Toyoda, J. T. Aubin et al., Influenza A/H5N1 virus infection in humans in Cambodia, Journal of Clinical Virology, vol.39, issue.3, pp.164-168, 2007.
DOI : 10.1016/j.jcv.2007.04.010
URL : https://hal.archives-ouvertes.fr/hal-00167807

P. Buchy, M. Fourment, S. Mardy, S. Sorn, D. Holl et al., Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004???2007, Emerging Infectious Diseases, vol.15, issue.10, pp.1641-1644, 2004.
DOI : 10.3201/eid1510.090115
URL : https://hal.archives-ouvertes.fr/pasteur-00808191

G. Cattoli, A. Fusaro, I. Monne, F. Coven, T. Joannis et al., Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry, Vaccine, vol.29, issue.50, pp.9368-9375, 2011.
DOI : 10.1016/j.vaccine.2011.09.127

D. Chessel, A. B. Dufour, and J. Thioulouse, The ade4 package-I-one-table methods, R News, vol.4, pp.5-10, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427558

A. J. Drummond, A. Rambaut, B. Shapiro, and O. G. Pybus, Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-1192, 2005.
DOI : 10.1093/molbev/msi103

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

Y. X. Fu and W. H. Li, Statistical tests of neutrality of mutations, Genetics, vol.133, pp.693-709, 1993.

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543
URL : https://hal.archives-ouvertes.fr/hal-00435028

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187

M. J. Greenacre, Theory and application of correspondence analysis, 1984.

M. J. Greenacre and J. Blasius, Multiple Correspondence Analysis and related Methods, 2006.
DOI : 10.1201/9781420011319

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser, vol.41, pp.95-98, 1999.

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

L. Kaufman and P. J. Rousseeuw, Finding Groups in Data: An Introduction to Cluster Analysis, 1990.
DOI : 10.1002/9780470316801

N. V. Kaverin, I. A. Rudneva, E. A. Govorkova, T. A. Timofeeva, A. A. Shilov et al., Epitope Mapping of the Hemagglutinin Molecule of a Highly Pathogenic H5N1 Influenza Virus by Using Monoclonal Antibodies, Journal of Virology, vol.81, issue.23, pp.12911-12917, 2007.
DOI : 10.1128/JVI.01522-07

M. Kimura, The Neutral Theory of Molecular Evolution, 1983.

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

M. Nei, Molecular EvolutionaryGenetics, 1987.

M. Nei and T. Gojobori, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions, Mol. Biol. Evol, vol.3, pp.418-426, 1986.

F. Pazos, A. Rausell, and A. Valencia, Phylogeny-independent detection of functional residues, Bioinformatics, vol.22, issue.12, pp.1440-1448, 2006.
DOI : 10.1093/bioinformatics/btl104

D. Posada and K. A. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

B. Shapiro, A. Rambaut, and A. J. Drummond, Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences, Molecular Biology and Evolution, vol.23, issue.1, pp.7-9, 2006.
DOI : 10.1093/molbev/msj021

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626

M. Tenenhaus and F. W. Young, An analysis and synthesis of multiple correspondence analysis, optimal scaling, dual scaling, homogeneity analysis and other methods for quantifying categorical multivariate data, Psychometrika, vol.25, issue.2, pp.91-119, 1985.
DOI : 10.1007/BF02294151

J. Thioulouse, D. Chessel, S. Doledec, and J. M. Olivier, ADE-4: a multivariate analysis and graphical display software, Statistics and Computing, vol.7, issue.1, pp.75-83, 1997.
DOI : 10.1023/A:1018513530268
URL : https://hal.archives-ouvertes.fr/hal-00434994

J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997.
DOI : 10.1093/nar/25.24.4876

M. D. Van-kerkhove, S. Vong, J. Guitan, D. Holl, P. Mangtani et al., Poultry movement networks in Cambodia: Implications for surveillance and control of highly pathogenic avian influenza (HPAI/H5N1), Vaccine, vol.27, issue.45, pp.6345-6352, 2009.
DOI : 10.1016/j.vaccine.2009.05.004

D. Vijaykrishna, J. Bahl, S. Riley, L. Duan, J. X. Zhang et al., Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses, PLoS Pathogens, vol.14, issue.9, p.1000161, 2008.
DOI : 10.1371/journal.ppat.1000161.s004

X. F. Wan, T. Nguyen, C. T. Davis, C. B. Smith, and Z. M. Zhao, Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between, e3462, 2001.

G. A. Watterson, On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975.
DOI : 10.1016/0040-5809(75)90020-9

W. Fao, Updated unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses, 2011.

X. Xu, K. Subbarao, N. J. Cox, and Y. Guo, Genetic Characterization of the Pathogenic Influenza A/Goose/Guangdong/1/96 (H5N1) Virus: Similarity of Its Hemagglutinin Gene to Those of H5N1 Viruses from the 1997 Outbreaks in Hong Kong, Virology, vol.261, issue.1, pp.96-111, 1999.
DOI : 10.1006/viro.1999.9820