Phylogenetic tree of the RCR Rep proteins. Maximum likelihood tree was constructed using the PhyML program , with the WAG evolutionary model  with gamma distribution of rates between sites (four categories, alpha estimated by PhyML). Sequence alignment was constructed using CLUSTALW . The nanovirus Rep was chosen as an outgroup to root the tree (see the main text for the outgroup selection). Numbers at the relevant branch-points represent bootstrap values (1000 replicates). Geminivirus-derived Rep of Nicotiana tabacum is underlined. The scale bar represents the number of amino acid substitutions per site.