P. Puigb-o, Y. I. Wolf, and E. V. Koonin, Search for a 'Tree of Life' in the thicket of the phylogenetic forest, J Biol, vol.8, issue.6, p.59, 2009.

E. V. Koonin and V. V. Dolja, Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol, Mol Biol Rev, vol.78, issue.2, p.24847023, 2014.

,

E. Corel, P. Lopez, R. Bapteste, and E. , Network-thinking: Graphs to analyze microbial complexity and evolution, Trends Microbiol, vol.24, issue.3, pp.224-261, 2016.
DOI : 10.1016/j.tim.2015.12.003
URL : https://hal.archives-ouvertes.fr/hal-01300043

,

R. L. Tatusov, M. Y. Galperin, D. A. Natale, and E. V. Koonin, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res, vol.28, issue.1, pp.33-39, 2000.

L. Li, C. J. Stoeckert, J. Roos, and D. S. , OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, issue.9, pp.2178-89, 2003.
DOI : 10.1101/gr.1224503
URL : http://genome.cshlp.org/content/13/9/2178.full.pdf

S. Fortunato, Community detection in graphs, Phys Rep, vol.486, issue.3-5, pp.75-174, 2010.
DOI : 10.1016/j.physrep.2009.11.002
URL : http://arxiv.org/pdf/0906.0612v1.pdf

,

S. Fortunato and D. Hric, Community detection in networks: A user guide, Phys Rep, vol.659, pp.1-44, 2016.
DOI : 10.1016/j.physrep.2016.09.002
URL : http://arxiv.org/pdf/1608.00163

M. Rosvall and C. T. Bergstrom, Multilevel Compression of Random Walks on Networks Reveals Hierarchical Organization in Large Integrated Systems, Plos One, vol.6, issue.4, 2011.

P. Zhang and C. Moore, Scalable detection of statistically significant communities and hierarchies, using message passing for modularity, Proc Natl Acad Sci, 2014.
DOI : 10.1073/pnas.1409770111
URL : http://www.pnas.org/content/111/51/18144.full.pdf

, , vol.111, pp.18144-18153

A. Lancichinetti, F. Radicchi, J. J. Ramasco, and S. Fortunato, Finding statistically significant communities in networks, Plos One, vol.6, issue.4, 2011.

F. Marquitti, P. R. Guimaraes, M. M. Pires, and L. F. Bittencourt, MODULAR: software for the autonomous computation of modularity in large network sets, Ecography, vol.37, issue.3, pp.221-225, 2014.

R. Monta~-nez and M. A. Medina, Sol e RV, Rodr ?guez-Caso C. When metabolism meets topology: Reconciling metabolite and reaction networks, Bioessays, vol.32, issue.3, pp.246-56, 2010.

, , 20127701.

G. Lima-mendez, J. Van-helden, A. Toussaint, and R. Leplae, Reticulate representation of evolutionary and functional relationships between phage genomes, Mol Biol Evol, vol.25, issue.4, pp.762-77, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01624306

H. B. Jang, F. F. Fagutao, S. W. Nho, S. B. Park, I. S. Cha et al., Phylogenomic network and comparative genomics reveal a diverged member of the PhiKZ-related group, marine vibrio phage PhiJM2012, J Virol, vol.87, issue.23, p.24067958, 2013.

,

J. Iranzo, M. Krupovic, and E. V. Koonin, The doublestranded DNA virosphere as a modular hierarchical network of gene sharing, MBio, vol.7, issue.4, pp.978-994, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977375

, , pp.978-994

J. Iranzo, E. V. Koonin, D. Prangishvili, and M. Krupovic, Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements, J Virol, vol.90, issue.24, pp.11043-55, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01375582

,

E. V. Koonin, V. V. Dolja, and M. Krupovic, Origins and evolution of viruses of eukaryotes: The ultimate modularity, Virology, pp.479-480, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977389

M. Kivela, A. Arenas, M. Barthelemy, J. P. Gleeson, Y. Moreno et al., Multilayer networks, J Comp Net, vol.2, issue.3, pp.203-71, 2014.

M. Fondi, A. Karkman, M. V. Tamminen, E. Bosi, M. Virta et al., Every gene is everywhere but the environment selects": Global geolocalization of gene sharing in environmental samples through network analysis, Genome Biol Evol, vol.8, issue.5, pp.1388-400, 2016.

,