BMC Genomics 2004, 5:69 http://www.biomedcentral.com/1471-2164/5/69 FUingruoroete1d 50% majority consensus tree from 4,000 ML trees sampled from the Bayesian posterior probability distribution Unrooted 50% majority consensus tree from 4,000 ML trees sampled from the Bayesian posterior probability distribution. Sup- port values are shown above the internode from Bayesian inference/distance bootstrap respectively. Only values above 50% are reported and values under 50% are indicated by (-). 100% values are indicated by (+). CDK names in blue are from organ- isms that fall into the "CTD-clade" in RPB1 phylogenetic analyses (see Fig. 2); and those in red are from groups in which the CTD is not strongly conserved. Inferred groups of CTD-directed CDKs 7, 8 and 9 are shown in bold. A large group of uniden- tified CDKs from Arabidopsis and Oryza, which appear to represent a plant-specific amplification of CTK9, were excluded from this analysis to determine whether identified plant CDK9s show a specific phylogenetic affinity to either the BUR1 or CTK1 subgroup. All identified plant sequences are included in an expanded analysis shown in additional file 1. Page 6 of 13 (page number not for citation purposes)