Evolution of DNA or amino acid sequences with dependent sites

Journal of Computational Biology

Volumn 5, Issue 1, 1998, Pages 149-163

  Von Haeseler, Arndt ^a   Schöniger, Michael ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; EVOLUTION; MODEL; PHYLOGENY; PRIORITY JOURNAL;

EID: 0031901451     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1998.5.149     Document Type: Article

References (41)

1. Adachi, J., and Hasegawa, M. 1996. Model of amino acid substitutions in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42, 459-468.
2. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J.D. 1994. Molecular Biology of the Cell. Garland, 3rd edition, New York.
3. Almagor, H. 1983. A Markov analysis of DNA sequences. J. Theor. Biol. 104, 633-645.
4. Avery, P.J. 1987. The analysis of intron data and their use in the detection of short signals. J. Mol. Evol. 26, 335-340.
5. Bhat, U.N. 1984. Elements of Applied Stochastic Processes. Wiley, 2nd edition, New York.
6. Blaisdell, B.E. 1985. Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eukaryotic nuclear DNA sequences both protein-coding and noncoding. J. Mol. Evol. 21, 278-288.
7. Chung, K.L. 1960. Markov Chains with Stationary Transition Probabilities. Springer, New York.
8. Cox, D.R. 1961. Tests of separate families of hypotheses. In Proceedings of the 4th Berkeley Symposium. Number 1, 105-123. University of California Press.
9. Cox, D.R. 1962. Further results on tests of separate families of hypotheses. J. Roy. Statist. Soc. B, 24, 406-424.
10. Dayhoff, M.O., ed. 1978. Atlas of Protein Sequence and Structure. Volume 5. Natl. Biomed. Res. Found, Silver Springs.
11. DeBry, R.W. 1992. The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol. 9, 537-551.
12. Elton, R.A. 1974. Theoretical models for heterogeneity of base composition in DNA. J. Theor. Biol. 45, 533-553.
13. Elton, R.A. 1975. Doublet frequencies in sequenced nucleic acids. J. Mol. Evol. 4, 323-346.
14. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17, 368-376.
15. Fitch, W.M. 1971. Towards defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20, 406-416.
16. Fitch, W.M. 1983. Random sequences. J. Mol. Biol. 163, 171-176.
17. Garden, P.W. 1980. Markov analysis of viral DNA/RNA sequences. J. Theor. Biol. 82, 679-684.
18. Goldman, N. 1993. Statistical tests of models of DNA substitutions. J. Mol. Evol. 36, 182-198.
19. Hasegawa, M., Kishino, H., and Yano, K. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
20. Huelsenbeck, J.P., and Hillis, D.M. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42, 247-264.
21. Jukes, T.H., and Cantor, C.R. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism. Munro, H.N., ed., 21-132. Academic Press, New York.
22. Karlin, K.S., and Taylor, H.M. 1981. A Second Course in Stochastic Processes. Academic Press Inc., London.
23. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
24. Kishino, H., Miyata, T., and Hasegawa, M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31, 151-160.
25. Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468.
26. Muse, S.V. 1995. Evolutionary analysis of DNA sequences subject to constraints on secondary structure. Genetics, 139, 1429-1439.
27. Rzhetsky, A. 1995. Estimating substitution rates in ribosomal RNA genes. Genetics, 141, 771-783.
28. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
29. Schöniger, M., and von Haeseler, A. 1993. A simple method to improve the reliability of tree reconstructions. Mol. Biol. Evol. 10, 471-483.
30. Schöniger, M., and von Haeseler, A. 1994a. A stochastic model for the evolution of autocorrelated DNA sequences. Mol. Phyl. Evol. 3, 240-247.
31. Schöniger, M., and von Haeseler, A. 1994b. Distance correction if sequence sites are not independently evolving. In Biometrische Probleme der Genomanalyse. Proceedings of the 1994 Workshop of the German Region of the International Biometric Society. Simianer, H. and Köhler, W., eds., 6-12. University of Hohenheim, Germany.
32. Schöniger, M., and von Haeseler, A. 1995. Performance of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when sequence sites are not independent. Syst. Biol. 44, 533-547.
33. Takezaki, N., and Nei, M. 1994. Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant. J. Mol. Evol. 39, 210-218.
34. Tateno, Y., Takezaki, N., and Nei, M. 1994. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11, 261-277.
35. Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In Some Mathematical Questions in Biology: DNA Sequence Analysis, Waterman, M.S., ed., 57-86. The American Mathematical Society, Providence, Rhode Island.
36. Tavaré, S., and Feng, Y. 1995. Reconstructing phylogenetic trees when sites are dependent. In Proceedings of the 4th Phlogeny Workshop, Tavaré, S., ed., number 95-48, 55-57. DIMACS, Center for Discrete Mathematics and Theoretical Computer Science, Princeton University, NJ.
37. Tavaré, S., and Giddings, B.W. 1989. Some statistical aspects of the primary structure of nucleotide sequences. In Mathematical Methods for DNA Sequences, Waterman, M.S., ed., 117-132. CRC Press, Boca Raton.
38. Tillier, E.R.M. 1994. Maximum likelihood with multiparameter models of substitutions. J. Mol. Evol. 39, 409-417.
39. Tillier, E.R.M., and Collins, R.A. 1995. Neighbor joining and maximum likelihood with RNA sequences: Addressing the interdependence of sites. Mol. Biol. Evol. 12, 7-15.
40. von Haeseler, A., and Schöniger, M. 1995. Reliability of tree reconstruction methods if sites are not evolving independently. In Proceedings of the 4th Phylogeny Workshop., Tavaré, S., ed., number 95-48, 65-68. DIMACS, Center for Discrete Mathematics and Theoretical Computer Science. Princeton University, NJ.
41. Zharkikh, A. 1994. Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol. 39, 315-329.