F. E. Angly, B. Felts, M. Breitbart, P. Salamon, and R. A. Edwards, The marine viromes of four oceanic regions, PLoS Biology, vol.4, p.368, 2006.

M. Pignatelli, G. Aparicio, I. Blanquer, V. Hernández, and A. Moya, Metagenomics reveals our incomplete knowledge of global diversity, Bioinformatics, vol.24, pp.2124-2125, 2008.

J. Raes, K. U. Foerstner, and P. Bork, Get the most out of your metagenome: computational analysis of environmental sequence data, Curr Opin Microbiol, vol.10, pp.490-498, 2007.

D. H. Huson, A. F. Auch, J. Qi, and S. C. Schuster, MEGAN analysis of metagenomic data, Genome Res, vol.17, pp.377-86, 2007.

L. B. Koski and G. B. Golding, The closest BLAST hit is often not the nearest neighbor, J Mol Evol, vol.52, pp.540-542, 2001.

C. Desnues, B. Rodriguez-brito, S. Rayhawk, S. Kelley, and T. Tran, Biodiversity and biogeography of phages in modern stromatolites and thrombolites, Nature, vol.452, pp.340-343, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02007337

E. A. Dinsdale, R. A. Edwards, D. Hall, F. Angly, and M. Breitbart, Functional metagenomic profiling of nine biomes, Nature, vol.452, pp.629-632, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02007369

F. Angly, B. Rodriguez-brito, D. Bangor, P. Mcnairnie, and M. Breitbart, PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information, BMC Bioinformatics, vol.6, p.41, 2005.

G. F. Steward, J. L. Montiel, and F. Azam, Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments, Limnol Oceanogr, vol.45, pp.1697-1706, 2000.

K. Holmfeldt, M. Middelboe, O. Nybroe, and L. Riemann, Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts, Appl Environ Microbiol, vol.73, pp.6730-6739, 2007.

R. Sandaa, Burden or benefit? Virus-host interactions in the marine environment, Res Microbiol, vol.159, pp.374-381, 2008.

M. G. Weinbauer and F. Rassoulzadegan, Are viruses driving microbial diversification and diversity?, Environ Microbiol, vol.6, pp.1-11, 2004.

L. M. Graves and B. Swaminathan, PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis, Int J Food Microbiol, vol.65, pp.55-62, 2001.

B. Diez, J. Antón, N. Guixa-boixereu, C. Pedrós-alió, and F. Rodriguez-valera, Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment, Int Microbiol, vol.3, pp.159-164, 2000.

J. Raes, J. Korbel, M. Lercher, V. Mering, C. Bork et al., Prediction of effective genome size in metagenomic samples, Genome Biol, vol.8, p.10, 2007.

R. Sandaa, F. Skjoldal, E. Bratbak, and G. , Virioplankton community structure along a salinity gradient in a solar saltern, Extremophiles, vol.7, pp.347-351, 2003.

K. E. Wommack, J. Ravel, R. T. Hill, J. Chun, and R. R. Colwell, Population dynamics of Chesapeake bay virioplankton: total-community analysis by pulsedfield gel electrophoresis, Appl Environ Microbiol, vol.65, pp.231-271, 1999.

J. Ranea, D. Buchan, J. M. Thornton, and C. A. Orengo, Evolution of protein superfamilies and bacterial genome size, J Mol Biol, vol.336, pp.871-87, 2004.

F. Rohwer and R. A. Edwards, The Phage Proteomic Tree: a genome-based taxonomy for phage, J Bacteriol, vol.184, pp.4529-4564, 2002.

P. Hugenholtz and G. W. Tyson, Microbiology: metagenomics, Nature, vol.455, pp.481-483, 2008.

K. E. Wommack, J. Bhavsar, and J. Ravel, Metagenomics: read length matters, Appl Environ Microbiol, vol.74, pp.1453-1463, 2008.

K. Rosario, S. Duffy, and M. Breitbart, Diverse circovirus-like genome architectures revealed by environmental metagenomics, J Gen Virol, vol.90, pp.2418-2424, 2009.

F. M. Lauro, D. Mcdougald, T. Thomas, T. J. Williams, and S. Egan, The genomic basis of trophic strategy in marine bacteria, Proc Nat Acad Sci, vol.106, pp.15527-15533, 2009.

K. T. Konstantinidis and J. M. Tiedje, Trends between gene content and genome size in prokaryotic species with larger genomes, Proc Nat Acad Sci, vol.101, pp.3160-3165, 2004.

D. Willner, R. V. Thurber, and F. Rohwer, Metagenomic signatures of 86 microbial and viral metagenomes, Environ Microbiol, vol.11, pp.1752-1766, 2009.

I. Hewson, D. M. Winget, K. E. Williamson, J. A. Fuhrman, and K. E. Wommack, Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida shelf (Gulf of Mexico), J Mar Biol Assoc UK, vol.86, pp.591-603, 2006.

E. A. Dinsdale, O. Pantos, S. Smriga, R. A. Edwards, and F. Angly, Microbial ecology of four coral atolls in the northern Line Islands, PLoS ONE, vol.3, p.1584, 2008.

P. Dassarma and S. Dassarma, On the origin of prokaryotic ''species'': the taxonomy of halophilic Archaea, Saline Syst, vol.4, p.5, 2008.

M. Dyall-smith, S. Tang, and C. Bath, Haloarchaeal viruses: how diverse are they?, Res Microbiol, vol.154, pp.309-313, 2003.

R. L. Vega-thurber, K. L. Barott, D. Hall, H. Liu, and B. Rodriguez-mueller, Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa, Proc Nat Acad Sci, vol.105, pp.18413-18418, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02007381

R. V. Thurber, D. Willner-hall, B. Rodriguez-mueller, C. Desnues, and R. A. Edwards, Metagenomic analysis of stressed coral holobionts, Environ Microbiol, vol.11, pp.2148-2163, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02008625

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J Mol Biol, vol.215, pp.403-413, 1990.

D. Rasko, G. Myers, and J. Ravel, Visualization of comparative genomic analyses by BLAST score ratio, BMC Bioinformatics, vol.6, issue.2, 2005.

R. Sadreyev and N. Grishin, COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance, J Mol Biol, vol.326, pp.317-336, 2003.

S. Karlin and S. F. Altschul, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes, Proc Nat Acad Sci, vol.87, pp.2264-2268, 1990.

B. Zybailov, A. L. Mosley, M. E. Sardiu, M. K. Coleman, and L. Florens, Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae, J Proteome Res, vol.5, pp.2339-2347, 2006.

L. Florens, M. J. Carozza, S. K. Swanson, M. Fournier, and M. K. Coleman, Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors, Methods, vol.40, pp.303-311, 2006.

A. C. Paoletti, T. J. Parmely, C. Tomomori-sato, S. Sato, and D. Zhu, Quantitative proteomic analysis of distinct mammalian mediator complexes using normalized spectral abundance factors, Proc Nat Acad Sci, vol.103, pp.18928-18933, 2006.

S. D. Bentley and J. Parkhill, Comparative genomic structure of prokaryotes, Annu Rev Genet, vol.38, pp.771-92, 2004.

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, pp.127-135, 2007.

R. Seshadri, S. A. Kravitz, L. Smarr, P. Gilna, and M. Frazier, CAMERA: a community resource for metagenomics, PLoS Biol, vol.5, p.75, 2007.

D. L. Wheeler, C. Chappey, A. E. Lash, D. D. Leipe, and T. L. Madden, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.28, pp.10-14, 2000.

F. Meyer, D. Paarmann, D. Souza, M. Olson, R. Glass et al., The metagenomics RAST server -a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, p.386, 2008.

, R: A language and environment for statistical computing, R Foundation for Statistical Computing