The phylogenetic tree of all RFX DBDs found in this study. Each distinct group of RFX is labeled. Labels for each putative RFX refer to records in Additional file 1. The colored branches indicate three major groups of RFX TFs: RFX1-3 in red, RFX4-6 in green, and RFX5-7 in blue. The fish RFX8 TFs cluster with the RFX1-3 group, while the fish RFX9 TFs cluster with the RFX5-7 group. All nematodes are grouped together (labeled DAF-19) with the RFX1-3 group. Some insects RFX TFs (labeled as dRFX) group with RFX1-3, while others (labeled dRFX1) with RFX5-7. M. brevicollis (cRFX1 and cRFX2) are shown in open squares (□). Drosophila dRFX2  is shown in the tree but it is not found in the sequenced D. melanogaster genome nor any sequenced Drosophila genome. It is likely located in the heterochromatic region (William Gelbart, personal communication). The phylogenetic tree was inferred using the Neighbor-Joining method . Phylogenetic analysis was performed using MEGA4 .