G. Devulder, G. Perrière, F. Baty, and J. P. Flandrois, BIBI, a Bioinformatics Bacterial Identification Tool, Journal of Clinical Microbiology, vol.41, issue.4, pp.1785-1787, 2003.
DOI : 10.1128/JCM.41.4.1785-1787.2003

URL : https://hal.archives-ouvertes.fr/hal-00427401

J. P. Flandrois, S. Mignard, E. Dantony, M. Gouy, and G. Devulder, Génération et visualisation de la phylogénie des Bacteria pour l'étude des incohérences taxinomiephylogénie, Proceedings of Journées Ouvertes Biologie Informatique Mathématiques, pp.277-285, 2005.

D. Harmsen, S. Dostal, A. Roth, S. Niemann, J. Rothganger et al., RIDOM: Comprehensive and public sequence database for identification of Mycobacteriumspecies, BMC Infectious Diseases, vol.50, issue.1, p.26, 2003.
DOI : 10.1099/00207713-50-5-1811

J. R. Cole, B. Chai, R. J. Farris, Q. Wang, S. A. Kulam et al., The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis, Nucleic Acids Research, vol.33, issue.Database issue, pp.294-296, 2005.
DOI : 10.1093/nar/gki038

D. Steinke, M. Vences, W. Salzburger, and A. Meyer, TaxI: a software tool for DNA barcoding using distance methods, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.2, issue.1, pp.360-1975, 1462.
DOI : 10.1186/1742-9994-2-5

L. Duret, G. Perrière, and M. Gouy, HOVERGEN: database and software for comparative analysis of homologous vertebrate genes, Bioinformatics Databases and Systems, pp.13-29, 1999.

A. M. Arigon, G. Perrière, and M. Gouy, HoSeqI: automated homologous sequence identification in gene family databases, Bioinformatics, vol.22, issue.14, pp.1786-1793, 2006.
DOI : 10.1093/bioinformatics/btl179

G. Perrière, L. Duret, and M. Gouy, HOBACGEN : database system for 10, 2000.

J. F. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-603, 2005.
DOI : 10.1093/bioinformatics/bti325

URL : https://hal.archives-ouvertes.fr/hal-00427861

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-52, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

J. R. Cole, B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-syed-mohideen et al., The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data, Nucleic Acids Research, vol.35, issue.Database, pp.169-72, 2007.
DOI : 10.1093/nar/gkl889

J. Wuyts, G. Perriere, and Y. Van-de-peer, The European ribosomal RNA database, Nucleic Acids Research, vol.32, issue.90001, pp.101-103, 2004.
DOI : 10.1093/nar/gkh065

URL : https://hal.archives-ouvertes.fr/hal-00427639

J. F. Robison-cox, M. M. Bateson, and D. M. Ward, Evaluation of nearestneighbor methods for detection of chimeric small-subunit rRNA sequences, Appl Environ Microbiol, issue.4, pp.61-1240, 1995.

G. A. Komatsoulis and M. S. Waterman, A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations, Appl Environ Microbiol, vol.63, issue.6, pp.2338-2384, 1997.

T. Huber, G. Faulkner, and P. Hugenholtz, Bellerophon: a program to detect chimeric sequences in multiple sequence alignments, Bioinformatics, vol.20, issue.14, pp.2317-2326, 2004.
DOI : 10.1093/bioinformatics/bth226

J. M. Gonzalez, J. Zimmermann, and C. Saiz-jimenez, Evaluating putative chimeric sequences from PCR-amplified products, Bioinformatics, vol.21, issue.3, pp.333-340, 2005.
DOI : 10.1093/bioinformatics/bti008

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman, At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies, Applied and Environmental Microbiology, issue.12, pp.11-7724, 2005.

K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman, New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras, Applied and Environmental Microbiology, vol.72, issue.9, pp.72-5734, 2006.
DOI : 10.1128/AEM.00556-06

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1563593

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

F. Corpet, Multiple sequence alignment with hierarchical clustering, Nucleic Acids Research, vol.16, issue.22, pp.10881-10890, 1988.
DOI : 10.1093/nar/16.22.10881

S. Abdeddaïm, Fast and sound two-step algorithms for multiple alignment of nucleic sequences, Proceedings IEEE International Joint Symposia on Intelligence and Systems, pp.179-192, 1997.
DOI : 10.1109/IJSIS.1996.565044

J. F. Dufayard, Incremental algorithms for the alignment and the phylogeny of large homologous sequence families, 2004.

R. C. Edgar, MUSCLE: amultiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

K. Howe, A. Bateman, and R. Durbin, QuickTree: building huge Neighbour-Joining trees of protein sequences, Bioinformatics, vol.18, issue.11, pp.1546-1547, 2002.
DOI : 10.1093/bioinformatics/18.11.1546

R. Desper and O. Gascuel, Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle, J. Comput. Biol, vol.19, pp.687-705, 2002.
URL : https://hal.archives-ouvertes.fr/lirmm-00269513

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

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