BMC Genomics 2004, 5:69 http://www.biomedcentral.com/1471-2164/5/69 performed in PHYLIP 3.573 [59], also using a JTT substi- tution model. Several a priori alternative hypotheses regarding CDK7 evolution were compared by KHT likelihood paired-sites tests [37]. Trees were constrained to require PfMRK from Plasmodium or GlCAKlike from Giardia, which previously have been characterized as a CDK7 orthologs [36,38], to group with the well-defined CDK7 clade. All most parsi- monious trees retaining these constrained relationships were tested against the fully resolved Bayesian consensus tree to determine whether the a priori hypotheses of orthologous relationships to CDK7 were significantly worse than the Bayesian consensus tree. Authors' contributions ZG was primarily responsible for database searching and assembly of CDK genes. ZG and JWS performed phyloge- netic analysis. ZG drafted the manuscript and figures and JWS contributed editorial revisions. All authors read and approved the final manuscript. Additional material Additional File 1 The single most likely tree, with branch lengths, recovered from 16,000 ML trees in the posterior probability distributions of four separate itera- tions of Bayesian inference. Thirty-two additional sequences were added to this analysis, and are indicated in bold in Table 1. They represent CDKs identified in incomplete genomes of organisms from which CTD structure is known, as well as a large amplification of apparent plant-specific orthologs of CDK9 from Arabidopsis and Oryza. The phylogenetic weight of these latter plant sequences disrupts inferred relationships among CDK9 orthologs as shown in Fig. 1. Support values are from Baye- sian inference and only values above 50% are shown. As in Fig. 1, CDK names in red are from groups in which the CTD is not strongly conserved, those in blue from members of the "CTD-clade." Inferred groups of CTD- directed CDKs 7, 8 and 9 are shown on the tree. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-5-69-S1.jpeg] Additional File 2 Original protein sequence alignment. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-5-69-S2.txt] Additional File 3 Edited protein sequence alignment. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-5-69-S3.txt] Acknowledgements The material is based on work supported by the National Science Founda- tion under grant MCB#0133295. We thank the suggestions of four anony- mous reviewers for advice that substantially improved this manuscript. References 1. Ekhdm SV, Reed SI: Regulation of G1 cyclin-dependent kinases in the mammalian cell cycle. Curr Opin Cell Biol 2000, 12:676-684. 2. Lees E: Cyclin dependent kinase regulation. Curr Opin Cell Biol 1995, 7:773-780. 3. Morgan DO: Principles of CDK regulation. Nature 1995, 374:131-134. 4. Harper JW, Adams PD: Cyclin-Dependent kinases. 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