Figure 4.

PhyML (Guindon and Gascuel, 2003) tree based on a PRANK alignment (Loytynoja and Goldman, 2005) of full-length RepA_C family protein sequences from WWTP Morges (names beginning with M) and Visp (names beginning with V), highlighted within gray shaded areas, with their most similar orthologs (GenBank entries with existing plasmid names in black; others in gray). Topology search using best of nearest neighbor interchanges and subtree pruning and regraftings, the LG model of amino acid substitution and discrete gamma model with four categories. Numbers at the nodes indicate the minimum of SH-like and χ²-based branch supports (Anisimova and Gascuel, 2006) (closer to one indicates stronger support). Outgroup is the RepA_C|EIJ25216.1| from Bifidobacterium longum subsp. longum 2-2B. A complete list of all assigned full names is available in Supplementary Table S11.