T

Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-95.

Takahata N. and Y. Satta. 1997. Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proc Natl Acad Sci USA 94:4811-4815.

Takahata, N. and Y. Satta. 1998. Footprints of intragenic recombination at HLA loci. Immunogenetics 47:430-441.

Takezaki, N., A. Rzhetsky,and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized tree. Mol. Biol. Evol. 12:823-833.

Tamura, K. and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Bio. Evol. 10:512-526.

Tavare, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lec. Math. Life Sci. 17:57-86.

Templeton, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-224.

Teng, S. C., B. Kim, and A. Gabriel. 1996. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383:641-644.

Tettelin H, N.J. Saunders, J. Heidelberg, A. C. Jeffries, K. E. Nelson, J. A. Eisen, K. A. Ketchum, D. W. Hood, P. J. Peden, R. J. Dodson, W. C. Nelson, M. L. Gwinn, R. DeBoy, J. D. Peterson, E. K. Hickey, D. H. Haft, S. L. Salzberg, O. White, R. D. Fleischmann, B. A. Dougherty, T. Mason, A. Ciecko, D. S. Parksey, E. Blair, H. Cittone, E. B. Clark, M. D. Cotton, T. R. Utterback, H. Khouri, H. Qin, J. Vamathevan, J. Gill, V. Scarlato, V. Masignani, M. Pizza, G. Grandi, L. Sun, H. O. Smith, C.M. Fraser, E. R. Moxon, R. Rappuoli, J. C. Venter. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287:1809-1815.

Tettelin, H., K. E. Nelson, I. Paulsen, J. A. Eisen, T. D. Read, S. Peterson, J. Heidelberg, R. T. DeBoy, D. H. Haft, R. J. Dodson, S. Durkin, M. Gwin, J. F. Kolonoay, W. C. Nelson, J. D. Peterson, L. A. Umayam, O. White, S. L. Salzberg, M. R. Lewis, D. Radune, E. Holtzapple, H. Khouri, A. M. Wolf, T. R. Utterback, C. K. Hansen, L. A. McDonald, T. V. Feldblyum, S. Angiuoli, T. Dickinson, E. K. Hickey, I. E. Holt, B. J. Loftus, F. Yang, H. O. Smith, J. C. Venter, B. A. Dougherty, D. A. Morrison, S.K. Hollingshead and C. M. Fraser. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498-506.

Thompson, J. D., Higgins, D. G. and Gibson, T. J. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. Clustal W

Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.

Thompson, J. D., F. Plewniak and O. Poch O. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27:2682-2690. Clustal W | Clustal X |

Thompson, S. M. 2007. An introduction to multiple sequence alignments - and the T-Coffee shop. Beyond just aligning sequences: How good can you make your alignment, and so what? in Bioinformatics for Systems Biology. Humana Press, Totowa, NJ.

Thorne, J. L., N. Goldman and D. T. Jones. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666-673.

Thorne, J. L. and H. Kishino. 2002. Divergence time and evolutionary rate estimation with multilocus data. Sys. Biol. 51:689-702.

Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.

Thursz, M. R., Thomas, H. C., Greenwood, B. M., and Hill, A. V. S. 1997. Heterozygote advantage for HLA class-II type in hepatitis B virus infection. Nature Genetics 17:11-12

Travisano, M. 1997. Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence. Genetics. 146(2):471-9.

Turner, P. E., C. L. Burch, K. A. Hanley, and L. Chao. 1999. Hybrid frequencies confirm limit to coinfection in the RNA bacteriophage phi6. J. Virology 73:2420-2424.

Turner, P. E. and L. Chao. 1998. Sex and the evolution of intrahost competition in RNA virus phi6. Genetics. 150(2):523-32.

Turner, P. E. and L. Chao. Prisoner's dilemma in an RNA virus. 1999. Nature. 398(6726):441-3.

Turner, P. E. and S. F. Elena. 2000. Cost of host radiation in an RNA virus. Genetics. 156:1465-70.

Turner, P. E. and L. Chao. 2003. Escape from Prisoner's Dilemma in RNA phage phi6. Am Nat. 161:497-505.