Bacteriophage phylogeny inferred from gene content. The tree was built using generalized average distance and neighbor-joining algorithm (see Methods). Large dots indicate clades inferred in the majority of resampled data sets. The branches leading to individual phages are colored according to their ICTV classification: family Siphoviridae is in magenta, Podoviridae is in orange, Myoviridae is in green, Fuselloviridae is in yellow, and Tectiviridae is in blue. The Bayesian tree displaying essentially the same phylogeny is presented in Fig. S1, available as Additional File 1. In the inner circle, the italicized, underlined colored numbers indicate 18 well-supported phage groups (see Supplementary Text for groups' description). They are followed by summary information of horizontal transfer events, where I stands transfer into the group, O for transfer from this group to another group, and W for transfer within the group. The algorithm for reconstructing these events is described in Methods and illustrated in Figure 2.