Homeodomain superfamily tree. This tree is based on a RaxML tree that included homeodomains from human, Drosophila, Mnemiopsis and a few related species that serve as place-holders for homeodomains known to be missing from human and Drosophila (see Figure 2 legend for species codes). This tree is referred to as a 'superfamily tree' as it includes homeodomains from all classes of the homeodomain superfamily, in contrast to the trees in Figures 2, 3 and 4 that include only homeodomains from individual classes. Mnemiopsis sequences are shown in red; human and other deuterostome sequences are shown in blue; Drosophila and other protostome sequences are shown in green; and cnidarian sequences are shown in brown. This RaxML tree had a higher likelihood value compared to several other methods and variations of starting trees supplied to RaxML (see methods). Collapsed clades represent clades with no Mnemiopsis representative and include a code that indicates how many deuterostome, protostome and cnidarian homeodomains are in that particular clade (for example, 2D4P1C would signify 2 deuterostome, 4 protostome, and 1 cnidarian). ML bootstraps are included for clades with bootstrap values greater than 50. Black dots appear on clades with Bayesian posterior probability values greater than 50 and red dots on clades greater than 90. Rooting of this tree is for display purposes only; branch lengths are presented uniformly, also for display purposes. Actual branch lengths can be viewed by opening the Newick-formatted tree file (Additional File 4), which also includes bootstrap and Bayesian support values, in a tree viewing/editing program such as FigTree .