Mouse bHLH super-tree for the 5 different clades and all 107 genes and relatedness presented. Clade B contains the inhibitory bHLH/Orange genes, as well as the Id genes. Clade E contains bHLH/PAS family genes. bHLH/bZip genes are spread throughout. Both the current and new nomenclature is presented. For some genes multiple older alternate names are listed with nearby branches (e.g. bHLHa 17, 18, 26, 27, 34) using the same new nomenclature, which indicates all are a single gene. Some new genes listed in Table S1 are not listed in the tree.