M. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-552, 2006.
DOI : 10.1080/10635150600755453
URL : https://hal.archives-ouvertes.fr/lirmm-00136658

A. Dereeper, V. Guignon, and G. Blanc, Phylogeny.fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Research, vol.36, issue.Web Server, pp.465-469, 2008.
DOI : 10.1093/nar/gkn180
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

C. Do, M. Mahabhashyam, M. Brudno, and S. Batzoglou, ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Research, vol.15, issue.2, 2005.
DOI : 10.1101/gr.2821705
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546535

R. 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
URL : http://doi.org/10.1093/nar/gkh340

D. Faulkner and J. Jurka, Multiple aligned sequence editor (MASE), Trends in Biochemical Sciences, vol.13, issue.8, pp.321-322, 1988.
DOI : 10.1016/0968-0004(88)90129-6

J. Felsenstein, Confidence Limits on Phylogenies: An Approach Using the Bootstrap, Evolution, vol.39, issue.4, pp.783-791, 1985.
DOI : 10.2307/2408678

J. Felsenstein, PHYLIP (phylogeny inference package) version 3.52. Distributed by the author, 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

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

M. Gouy and S. Delmotte, Remote access to ACNUC nucleotide and protein sequence databases at PBIL, Biochimie, vol.90, issue.4, pp.555-562, 2008.
DOI : 10.1016/j.biochi.2007.07.003
URL : https://hal.archives-ouvertes.fr/hal-00428117

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

D. Higgins, A. Bleasby, and R. Fuchs, CLUSTAL V: improved software for multiple sequence alignment, Bioinformatics, vol.8, issue.2, pp.189-191, 1992.
DOI : 10.1093/bioinformatics/8.2.189

J. Lake, Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances., Proceedings of the National Academy of Sciences, vol.91, issue.4, pp.1455-1459, 1994.
DOI : 10.1073/pnas.91.4.1455
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC43178/pdf

M. Larkin, G. Blackshields, and N. Brown, Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948
DOI : 10.1093/bioinformatics/btm404
URL : https://hal.archives-ouvertes.fr/hal-00206210

W. Li, Unbiased estimation of the rates of synonymous and nonsynonymous substitution, Journal of Molecular Evolution, vol.3, issue.1, pp.96-99, 1993.
DOI : 10.1007/BF02407308

D. Maddison, D. Swofford, and W. Maddison, Nexus: An Extensible File Format for Systematic Information, Systematic Biology, vol.46, issue.4, pp.590-621, 1997.
DOI : 10.1093/sysbio/46.4.590

J. Maizel, . Jr, and R. Lenk, Enhanced graphic matrix analysis of nucleic acid and protein sequences., Proceedings of the National Academy of Sciences, vol.78, issue.12, pp.7665-7669, 1981.
DOI : 10.1073/pnas.78.12.7665

M. Nei, C. Notredame, D. Higgins, and J. Heringa, Molecular evolutionary genetics T-Coffee: a novel method for multiple sequence alignments, J Mol Biol, vol.302, pp.205-217, 1987.

W. Pearson and D. Lipman, Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2444-2448, 1988.
DOI : 10.1073/pnas.85.8.2444

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

A. Rzhetsky and M. Nei, Tests of applicability of several substitution models for DNA sequence data., Molecular Biology and Evolution, vol.12, issue.1, pp.131-151, 1995.
DOI : 10.1093/oxfordjournals.molbev.a040182

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.

J. Studier and K. Keppler, A note on the neighbor-joining algorithm of Saitou and Nei, Mol Biol Evol, vol.5, pp.729-731, 1988.

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092
URL : http://mbe.oxfordjournals.org/cgi/content/short/24/8/1596