Phylogeny of LIM homeobox genes. The maximum likelihood tree based on an alignment of two LIM domains and the homeodomain is shown here with support values from Neighbor-joining/Likelihood/Bayesian analyses shown for the major nodes (relationships within the major classes were well supported only for vertebrate sequences). Neighbor-joining and Likelihood bootstrap values above 50% are shown, as are Bayesian posterior probabilities above 0.95. Full trees from each analysis are shown in Additional file 1. Aq = Amphimedon queenslandica(blue); Ce = Caenorhabditis elegans; Dm = Drosophila melanogaster; Dr = Danio rerio; Hm = Hydra magnipapillata (orange); Hs = Homo sapiens; Nv = Nematostella vectensis (green); Rn = Rattus norvegicus; Sp = Strongylocentrotus purpuratus; Ta = Trichoplax adhaerens (red); Xt = Xenopus tropicalis.