Phylogenetic analysis of the cnidarian bHLHs related to the Twist and Atonal superfamilies. The represented tree is a NJ tree, which has been rooted using a human bHLH sequence from the MyoD family as an outgroup. This tree is based on a multiple alignment that only includes the bHLH sequences of Drosophila melanogaster (in yellow) and Homo sapiens (in orange) which constitute the families belonging to the Atonal and Twist superfamilies  and their relatives in Nematostella vectensis (in light green) and Hydra magnipapillata (in dark green). The Atonal superfamily includes the Atonal, Neurogenin, NeuroD, Net, Oligo, Beta3, Delilah, and Mist families; the Twist superfamily includes the Twist, Paraxis, Hand, PTFa, PTFb, MyoRa, MyoRb, SCL, and NSCL families. Similar relationships (with similar statistical supports) were found when we used the entire set of bHLH genes of these 4 aforementioned species. The different metazoan families of orthologs are indicated in blue. Numbers above the internal branches are their statistical support values obtained with different methods of phylogenetic reconstruction: first number = bootstrap support in neighbour-joining analysis (10,000 bootstrap replicates); second number = bootstrap support in maximum-likelihood analysis (150 bootstrap replicates); third number = posterior probabilities in Bayesian inference-based analysis. Only statistical support values >50% are shown except for a few cases. Other internal branches (with statistical support <50%) should be considered unreliable. Statistical supports for the existence of the different families are shown in blue. We can see that 7 families (indicated by red asterisks) out of the 18 that are shown on this tree, have cnidarian members and that several cnidarian bHLHs cannot be assigned to any of these families. Some of these bHLHs form monophyletic groups comprising sequences from either one or both of the two cnidarian species (indicated by dark green numbers, from 1 to 6). Group 1 is comprised of only Nematostella vectensis sequences and groups 2 to 9 are comprised of at least one representative from both Nematostella vectensis and Hydra magnipapillata. Group 2 may correspond to Delilah genes, group 3 to Oligo/Beta3/Mist genes, and group 4 to NeuroD/Neurogenin genes (see additional files 13 and 14 for more details).