Maximum likelihood phylogeny of 113 representative SET-domain sequences. Bootstrap values for the major SET-domain families that are higher than 60% by either of the maximum likelihood (ML) or the maximum parsimony (MP) methods are shown at the node (the two % values are ML/MP). Internal branches supporting the major SET-domain families with higher than 80% ML bootstrap values are also indicated by thick lines. Within the major SET-domain protein groups, bootstrap values by the ML analysis greater than 60%, 70%, 80%, and 90% are indicated by stars (*), filled circles (●), filled squares (■), and filled triangles (▲), respectively. SET-domain protein subgroups discussed in the main text are indicated by numbers. Representative domain names are shown for the major SET-domain protein families (see Additional file 3 for the domain names). Species abbreviations are given in Additional file 1. For this ML phylogeny, the gamma shape parameter and the proportion of invariant sites were estimated to be 0.779 and 0, respectively.