Phylogenetic distance tree of RNA polymerases. RNA polymerase sequences are taken from accession data as described in the Methods section. The unrooted tree was constructed by the neighbour-joining method using PAUP*4b10  and the default settings. Numbers on the branches indicate the percentages of bootstrap support indicated by a heuristic search with 100 random addition replicates and the tree-bisection-reconnection branch-swapping algorithm. All bootstrap values > 50 have been reported except where they occur within the three well-supported RNA polymerase I (rpo1), RNA polymerase II (rpo2) and RNA polymerase III (rpo3) groups. RNA polymerases that contain an intein are indicated by asterisks (*); strains of the E. huxleyi virus are polymorphic for the presence of an intein in RNA polymerase (*/-). The alignment used is available as supplementary data (additional file 1).