I. Kalvari, E. P. Nawrocki, J. Argasinska, N. Quinones-olvera, R. D. Finn et al., Non-coding RNA analysis using the RFAM database, Current protocols in bioinformatics, vol.62, p.51, 2018.

L. Zheng, J. Li, J. Wu, W. Sun, S. Liu et al., deepBase v2. 0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data, Nucleic acids research, vol.44, issue.D1, pp.196-202, 2015.

J. S. Mccaskill, The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers: Original Research on Biomolecules, vol.29, issue.6-7, pp.1105-1119, 1990.

P. Clote, Y. Ponty, and J. Steyaert, Expected distance between terminal nucleotides of RNA secondary structures, Journal of mathematical biology, vol.65, pp.581-599, 2012.
URL : https://hal.archives-ouvertes.fr/inria-00619921

E. Freyhult, V. Moulton, and P. Clote, RNAbor: a web server for RNA structural neighbors, Nucleic acids research, vol.35, pp.305-309, 2007.

R. Lorenz, C. Flamm, and I. L. Hofacker, 2d projections of RNA folding landscapes, 2009.

J. Waldispühl, S. Devadas, B. Berger, and P. Clote, RNAmutants: a web server to explore the mutational landscape of RNA secondary structures, Nucleic acids research, vol.37, pp.281-286, 2009.

I. Miklós, I. M. Meyer, and B. Nagy, Moments of the boltzmann distribution for RNA secondary structures, Bulletin of mathematical biology, vol.67, pp.1031-1047, 2005.

Y. Ponty and C. Saule, A combinatorial framework for designing (pseudoknotted) RNA algorithms, Algorithms in Bioinformatics, pp.250-269, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00601060

J. Qin, M. Fricke, M. Marz, P. F. Stadler, and R. Backofen, Graphdistance distribution of the boltzmann ensemble of RNA secondary structures, Algorithms for molecular biology : AMB, vol.9, p.19, 2014.

Y. Ding and C. E. Lawrence, A statistical sampling algorithm for RNA secondary structure prediction, Nucleic acids research, vol.31, pp.7280-7301, 2003.

R. Lorenz, S. H. Bernhart, C. Höner-zu-siederdissen, H. Tafer, C. Flamm et al., ViennaRNA package 2.0, Algorithms for molecular biology : AMB, vol.6, p.26, 2011.

J. S. Reuter and D. H. Mathews, RNAstructure: software for RNA secondary structure prediction and analysis, BMC bioinformatics, vol.11, p.129, 2010.

N. R. Markham and M. Zuker, UNAFold: software for nucleic acid folding and hybridization, Methods in molecular biology, vol.453, pp.3-31, 2008.

W. A. Lorenz and P. Clote, Computing the partition function for kinetically trapped RNA secondary structures, PloS one, vol.6, p.16178, 2011.

J. Michálik, H. Touzet, and Y. Ponty, Efficient approximations of RNA kinetics landscape using non-redundant sampling, Bioinformatics, vol.33, pp.283-292, 2017.

J. Waldispühl and Y. Ponty, An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure, Journal of computational biology : a journal of computational molecular cell biology, vol.18, pp.1465-1479, 2011.

M. Kucharík, I. L. Hofacker, P. F. Stadler, and J. Qin, Basin hopping graph: a computational framework to characterize RNA folding landscapes, Bioinformatics, vol.30, 2009.

S. Pei, J. S. Anthony, and M. M. Meyer, Sampled ensemble neutrality as a feature to classify potential structured RNAs, BMC genomics, vol.16, p.35, 2015.

A. Spasic, S. M. Assmann, P. C. Bevilacqua, and D. H. Mathews, Modeling RNA secondary structure folding ensembles using SHAPE mapping data, Nucleic acids research, vol.46, pp.314-323, 2018.

S. Washietl, I. L. Hofacker, P. F. Stadler, and M. Kellis, Rna folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction, Nucleic acids research, vol.40, pp.4261-4272, 2012.

V. Reinharz, Y. Ponty, and J. Waldispühl, A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution, Bioinformatics, vol.29, pp.308-315, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00840260

B. Voss, R. Giegerich, and M. Rehmsmeier, Complete probabilistic analysis of RNA shapes, BMC biology, vol.4, issue.5, 2006.

D. Gardy and Y. Ponty, Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models, GASCOM -8th conference on random generation of combinatorial structures -2010. Montréal, Canada: LACIM, UQAM, p.14, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00543150

J. Boisberranger, D. Gardy, and Y. Ponty, The weighted words collector, AOFA -23rd International Meeting on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms -2012, ser. DMTCS Proceedings, Nicolas, Broutin, Luc, and Devroye, pp.243-264, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00666399

W. A. Lorenz and Y. Ponty, Non-redundant random generation algorithms for weighted context-free grammars, Theoretical Computer Science, vol.502, pp.177-194, 2013.

D. H. Turner and D. H. Mathews, NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic acids research, vol.38, pp.280-282, 2010.

M. Zuker and D. Sankoff, RNA secondary structures and their prediction, Bulletin of mathematical biology, vol.46, issue.4, pp.591-621, 1984.

S. Will, K. Reiche, I. Hofacker, P. Stadler, and R. Backofen, Inferring noncoding RNA families and classes by means of genomescale structure-based clustering, PLoS Comput. Biol, vol.3, p.65, 2007.

J. N. Zadeh, B. R. Wolfe, and N. A. Pierce, Nucleic acid sequence design via efficient ensemble defect optimization, Journal of Computational Chemistry, vol.32, issue.3, pp.439-52, 2011.

J. Michalik, Non-redundant sampling in RNA bioinformatics, 2019.
URL : https://hal.archives-ouvertes.fr/tel-02124550

S. Janssen and R. Giegerich, The RNA shapes studio, Bioinformatics, vol.31, pp.423-425, 2015.

, Faster computation of exact RNA shape probabilities, Bioinformatics, vol.26, pp.632-639, 2010.

M. Vingron and P. Argos, Determination of reliable regions in protein sequence alignments, Protein engineering, vol.3, pp.565-569, 1990.

E. Jacox, C. Chauve, G. J. Szöll?si, Y. Ponty, and C. Scornavacca, ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony, Bioinformatics, vol.32, pp.2056-2058, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01276903

C. Chauve, J. Courtiel, and Y. Ponty, Counting, generating, analyzing and sampling tree alignments, International Journal of Foundations of Computer Science, vol.29, issue.05, pp.741-767, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01500116