@. Minimum, L. Of, and A. Block, 10 ? Allowed Gap Positions: With Half ? Use Similarity Matrices: Yes See Additional file 1: Figure S6 for a detailed view of the aligned sequences and the conserved sub-sequences

O. Leyser, Dynamic Integration of Auxin Transport and Signalling, Current Biology, vol.16, issue.11, pp.424-457, 2006.
DOI : 10.1016/j.cub.2006.05.014

T. Guilfoyle and G. Hagen, Auxin response factors, Current Opinion in Plant Biology, vol.10, issue.5, pp.453-60, 2007.
DOI : 10.1016/j.pbi.2007.08.014

D. Remington, T. Vision, T. Guilfoyle, and J. Reed, Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families, PLANT PHYSIOLOGY, vol.135, issue.3, pp.1738-52, 2004.
DOI : 10.1104/pp.104.039669

T. Vernoux, G. Brunoud, E. Farcot, V. Morin, H. Van-den-daele et al., The auxin signalling network translates dynamic input into robust patterning at the shoot apex, Molecular Systems Biology, vol.127, issue.1, p.508, 2011.
DOI : 10.1242/dev.054973
URL : https://hal.archives-ouvertes.fr/hal-00828880

J. Joung, E. Ramm, and C. Pabo, A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions, Proceedings of the National Academy of Sciences, vol.97, issue.13, pp.7382-7389, 2000.
DOI : 10.1073/pnas.110149297

J. Daudin, F. Picard, and R. S. , A mixture model for random graphs, Statistics and Computing, vol.4, issue.2, pp.173-8310, 2007.
DOI : 10.1007/s11222-007-9046-7
URL : https://hal.archives-ouvertes.fr/inria-00070186

M. Mariadassou, R. S. Vacher, and C. , Uncovering latent structure in valued graphs: A variational approach, The Annals of Applied Statistics, vol.4, issue.2, pp.715-757, 2010.
DOI : 10.1214/07-AOAS361SUPP
URL : https://hal.archives-ouvertes.fr/hal-01197514

R. Kass and A. Raftery, Bayes Factors, Journal of the American Statistical Association, vol.2, issue.430, pp.773-95, 1995.
DOI : 10.1080/01621459.1995.10476572

H. Kriegel, P. Kröger, J. Sander, and A. Zimek, Density-based clustering, Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, vol.28, issue.3, pp.231-271, 2011.
DOI : 10.1002/widm.30

J. Thompson, D. Higgins, and T. 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.4673-80, 1994.
DOI : 10.1093/nar/22.22.4673

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

M. Nanao, T. Vinos-poyo, G. Brunoud, E. Thévenon, M. Mazzoleni et al., Structural basis for oligomerization of auxin transcriptional regulators, Nature Communications, vol.15, pp.3617-3627, 2014.
DOI : 10.1038/ncomms4617
URL : https://hal.archives-ouvertes.fr/hal-00984482

D. Korasick, C. Westfall, S. Lee, M. Nanao, R. Dumas et al., Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression, Proceedings of the National Academy of Sciences, vol.111, issue.14, pp.5427-5459, 2014.
DOI : 10.1073/pnas.1400074111
URL : https://hal.archives-ouvertes.fr/hal-00984283

M. Han, Y. Park, I. Kim, E. Kim, T. Yu et al., Structural basis for the auxin-induced transcriptional regulation by Aux/IAA17, Proceedings of the National Academy of Sciences, vol.111, issue.52, pp.18613-18621, 2014.
DOI : 10.1073/pnas.1419525112

D. Dinesh, M. Kovermann, M. Gopalswamy, A. Hellmuth, C. Villalobos et al., Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response, Proceedings of the National Academy of Sciences, vol.112, issue.19
DOI : 10.1073/pnas.1424077112

C. Shen, S. Wang, Y. Bai, Y. Wu, S. Zhang et al., Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.), Journal of Experimental Botany, vol.61, issue.14, pp.3971-81, 2010.
DOI : 10.1093/jxb/erq208

C. Fraley and A. Raftery, MCLUST Version 3 for R: Normal Mixture Modeling and Model-Based Clustering, 2006.

K. Nowicki and T. Snijders, Estimation and Prediction for Stochastic Blockstructures, Journal of the American Statistical Association, vol.96, issue.455, pp.1077-87, 2001.
DOI : 10.1198/016214501753208735

J. Leger and . Wmixnet, Software for clustering the nodes of binary and valued graphs using the stochastic block model

A. Dempster, N. Laird, and D. Rubin, Maximum likelihood from incomplete data via the EM algorithm, J R Stat Soc Ser B, vol.39, pp.1-38, 1977.

L. Kaufman and P. Rousseeuw, Finding groups in data: an introduction to cluster analysis, 1990.
DOI : 10.1002/9780470316801

E. Chapman and E. M. , Mechanism of Auxin-Regulated Gene Expression in Plants, Annual Review of Genetics, vol.43, issue.1, pp.265-85, 2009.
DOI : 10.1146/annurev-genet-102108-134148

G. Hagen and T. Guilfoyle, Auxin-responsive gene expression: genes, promoters and regulatory factors, Plant Mol Biol, vol.49, pp.3-4373, 2002.
DOI : 10.1007/978-94-010-0377-3_9