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Phages are viruses infecting prokaryotes. The sub-group of temperate phages has the capability to remain in their host, in a latent stage, as prophages. Most of the prophages are found integrated in the host chromosome while some are established as plasmids. Whether functional or defective, prophages can recombine with other phages and/or prophages, a central mechanism in bacteriophage evolution (Hendrix et al., 1999). Source text: Lima-Mendez et al., 2008.