A. Brady and S. Salzberg, Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models, Nature Methods, vol.25, issue.9, 2009.
DOI : 10.1093/nar/27.23.4636

D. Huson, A. Auch, J. Qi, and S. Schuster, MEGAN analysis of metagenomic data, Genome Research, vol.17, issue.3, 2007.
DOI : 10.1101/gr.5969107

E. Karsenti and T. O. Consortium, A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, 2011.
DOI : 10.1371/journal.pbio.1001177.g002
URL : https://hal.archives-ouvertes.fr/hal-00691580

J. Pley, R. Andonov, J. Gibrat, A. Marin, and V. Poirriez, Parallélisations d'une méthode de reconnaissance de repliements de protéines (frost) JOBIM, 2002.

M. Krupovic, H. Dennis, and . Bamford, Double-stranded dna viruses: 20 families and only five different architectural principles for virion assembly. Current Opinion in Virology, 2011.
DOI : 10.1016/j.coviro.2011.06.001

E. Papandreou, . Eliopoulos, A. Berezovsky, E. Lopes, J. Eliopoulos et al., Universal positions in globular proteins. From observation to simulation, European Journal of Biochemistry, vol.295, issue.23-24, 2004.
DOI : 10.1016/S0959-440X(97)80002-4
URL : https://hal.archives-ouvertes.fr/hal-00086581

. Patil, R. Kaustubh, . Haider, . Peter, P. B. Pope et al., Taxonomic metagenome sequence assignment with structured output models, Nature Methods, vol.8, issue.3, 2011.
DOI : 10.1038/nmeth.1358

S. Cheng and C. Brooks, 3rd viral capsid proteins are segregated in structural fold space, PLoS Comput Biol, 2013.

A. Curtis and . Suttle, Marine viruses ? major players in the global ecosystem, Nature Reviews Microbiology, 2007.