H. Hori and S. Osawa, Origin and Evolution of Organisms as Deduced from 5s Ribosomal RNA Sequences, Molecular biology and evolution, vol.4, issue.5, pp.445-472, 1987.

F. Johansson, mpmath: a Python library for arbitrary-precision floating-point arithmetic (version 0.14), 2010.

V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz, Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environmental Microbiology, vol.64, issue.1, pp.118-141, 2010.
DOI : 10.1111/j.1462-2920.2009.02051.x

K. Lari and S. Young, The estimation of stochastic context-free grammars using the Inside-Outside algorithm, Computer Speech & Language, vol.4, issue.1, pp.35-560885, 1990.
DOI : 10.1016/0885-2308(90)90022-X

N. Leontis and E. Westhof, Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001.
DOI : 10.1017/S1355838201002515

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1667, 2006.
DOI : 10.1093/bioinformatics/btl158

P. Medvedev, E. Scott, B. Kakaradov, and P. Pevzner, Error correction of high-throughput sequencing datasets with non-uniform coverage, Bioinformatics, vol.27, issue.13, pp.137-178, 2011.
DOI : 10.1093/bioinformatics/btr208

G. Olsen, D. Lane, N. Giovannoni, . Pace, and . Stahl, Microbial ecology and evolution: a ribosomal RNA approach. Annual review of microbiology, pp.337-65, 1986.

G. Olsen and C. Woese, Ribosomal RNA: a key to phylogeny, The FASEB journal, vol.7, issue.1, pp.113-123, 1993.

C. Quince, A. Lanzén, P. Thomas, . Curtis, J. Russell et al., Accurate determination of microbial diversity from 454 pyrosequencing data, Nature Methods, vol.25, issue.9, pp.639-680, 2009.
DOI : 10.1093/nar/gkh340

A. Quinlan, D. Stewart, G. Strömberg, and . Marth, Pyrobayes: an improved base caller for SNP discovery in pyrosequences, Nature Methods, vol.8, issue.2, pp.179-81, 2008.
DOI : 10.1016/0888-7543(88)90007-9

J. Stombaugh, L. Craig, E. Zirbel, . Westhof, B. Neocles et al., Frequency and isostericity of RNA base pairs, Nucleic Acids Research, vol.37, issue.7, pp.2294-312, 2009.
DOI : 10.1093/nar/gkp011
URL : https://hal.archives-ouvertes.fr/hal-00484475

J. Peter, . Turnbaugh, E. Ruth, M. Ley, C. M. Hamady et al., The Human Microbiome Project, Nature, issue.7164, pp.449804-449814, 2007.

H. Douglas, . Turner, H. David, and . Mathews, NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Database issue), pp.280-282, 2010.

J. Waldispühl, S. Devadas, B. Berger, and P. Clote, Efficient Algorithms for Probing the RNA Mutation Landscape, PLoS Computational Biology, vol.67, issue.245, p.1000124, 2008.
DOI : 10.1371/journal.pcbi.1000124.s001

E. Zuckerkandl and L. Pauling, Molecules as documents of evolutionary history, Journal of Theoretical Biology, vol.8, issue.2, pp.357-366, 1965.
DOI : 10.1016/0022-5193(65)90083-4