PAGE 9 OF 9 8. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coﬀee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 13. 9. Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (2000) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 8. 10. Edgar,R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 6. 11. Lassmann,T. and Sonnhammer,E.L. (2005) Kalign–an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics, 6, 298. 12. Felsenstein,J. (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164–166. 13. Swoﬀord,D.L. (2002) PAUP . Phylogenetic Analysis Using Parsimony ( and Other Methods). Sinauer Associates, Sunderland, Massachusetts. 14. Cartwright,R.A. (2005) DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics, 21 (Suppl. 3), iii31–iii38. 15. Hasegawa,M., Kishino,H. and Yano,T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160–174. 16. Li,H., Coghlan,A., Ruan,J., Coin,L.J., Heriche,J.K., Osmotherly,L., Li,R., Liu,T. and Zhang,Z. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res., 34, D572–D580. 17. Karlin,S. and Burge,C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet., 11, 283–290. 18. Karlin,S. (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol., 1, 598–610. 19. Kishino,H. and Hasegawa,M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol., 29, 10. 20. Jukes,T.H. and Cantor,C.R. (1969) Evolution of protein molecules. In Munro,H.N. (ed.), Mammalian Protein Metabolism, Academic Press, New York, pp. 21–132. Nucleic Acids Research, 2008, Vol. 36, No. 5 e33 21. Kimura,M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 10. 22. Tamura,K. and Nei,M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. J. Mol. Evol., 10, 512–526. 23. Hollich,V., Milchert,L., Arvestad,L. and Sonnhammer,E.L. (2005) Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. J. Mol. Evol., 22, 2257–2264. 24. Penny,D. and Hendy,M.D. (1985) The use of tree comparison metrics. Syst. Zool., 34, 12. 25. Li,W.-H. (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA. 26. Huelsenbeck,J.P., Larget,B. and Alfaro,M.E. (2004) Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol., 21, 1123–1133. 27. Bos,D.H. and Posada,D. (2005) Using models of nucde evolution to leotibuild phylogenetic trees. Dev. Comp. Immunol., 29, 211–227. 28. Posada,D. (2006) ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res., 34, W700–W703. 29. Zhang,Z. and Gerstein,M. (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res., 31, 5338–5348. 30. Saitou,N. and Ueda,S. (1994) Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates. Mol. Biol. Evol., 11, 504–512. 31. Vinga,S. and Almeida,J. (2003) Alignment-free sequence comparison-a review. Bioinformatics, 19, 513–523. 32. Morrison,D.A. (2007) A review of: ‘the tree of life: a phylogenetic classiﬁcation’. Syst. Biol., 56, 696–698. 33. Rokas,A. (2006) Genomics. Genomics and the tree of life. Science (New York), 313, 1897–1899.