A Dirichlet process model for detecting positive selection in protein-coding DNA sequences

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 16, 2006, Pages 6263-6268

  Huelsenbeck, John P ^a   Jain, Sonia ^b   Frost, Simon W D ^b   Pond, Sergei L Kosakovsky ^b  

^a University of California at San Diego   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; DNA SEQUENCE; MOLECULAR MODEL; NATURAL SELECTION; POPULATION GENETICS; PRIORITY JOURNAL; PROBABILITY; TECHNIQUE; THEORETICAL STUDY;

ANIMALS; BAYES THEOREM; DNA; MODELS, GENETIC; OPEN READING FRAMES; PROTEINS; SELECTION (GENETICS);

EID: 33646586721     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0508279103     Document Type: Article

References (40)

1. Hughes, A. & Nei, M. (1988) Nature 335, 167-170.
2. Nielsen, R. & Yang, Z. (1998) Genetics 148, 929-936.
3. Lee, Y. H., Ota, T. & Vaquier, V. (1995) Mol. Biol. Evol. 12, 231-238.
4. Messier, W. & Stewart, C. B. (1997) Nature 385, 151-154.
5. Miyata, T. & Yasunaga, T. (1980) J. Mol. Evol. 16, 23-36.
6. Nei, M. & Gojobori, T. (1986) Mol. Biol. Evol. 3, 418-426.
7. Li, W. H., Wu, M. & Luo, C. L. (1985) Mol. Biol. Evol. 2, 150-174.
8. Li, W. H. (1993) J. Mol. Evol. 36, 96-99.
9. Pamilo, P. & Blanchi, N. O. (1993) Mol. Biol. Evol. 10, 271-281.
10. Comeron, J. M. (1995) J. Mol. Evol. 41, 1152-1159.
11. Ina, Y. (1995) J. Mol. Evol. 40, 190-226.
12. Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A. (2000) Mol. Biol. Evol. 17, 32-43.
13. Yang, Z. & Nielsen, R. (2000) Genetics 155, 431-449.
14. Goldman, N. & Yang, Z. (1994) Mol. Biol. Evol. 11, 725-736.
15. Muse, S. V. & Gaut, B. S. (1994) Mol. Biol. Evol. 11, 715-724.
16. Yang, Z. (1998) Mol. Biol. Evol. 15, 568-573.
17. Fitch, W. M., Bush, R. M., Bender, C. A. & Cox, N. J. (1997) Proc. Natl. Acad. Sci. USA 94, 7712-7718.
18. Suzuki, Y. & Gojobori, T. (1999) Mol. Biol. Evol. 16, 1315-1328.
19. Pond, S. K. & Muse, S. V. (2005) Mol. Biol. Evol. 22, 2375-2385.
20. Pond, S. L. K. & Frost, S. D. W. (2005) Mol. Biol. Evol. 22, 1208-1222.
21. Crandall, K. A., Kelsey, C. R., Imamichi, H., Lane, H. C. & Salzman, N. P. (1999) Mol. Biol. Evol. 16, 372-382.
22. Sawyer, S. & Hartl, D. (1992) Genetics 132, 1161-1176.
23. Nielsen, R. & Yang, Z. (2003) Mol. Biol. Evol. 20, 1231-1239.
24. Lartillot, N. & Philippe, H. (2004) Mol. Biol. Evol. 21, 1095-1109.
25. Pond, S. L. K. & Frost, S. D. W. (2005) Mol. Biol. Evol. 22, 223-234.
26. Zanotto, P. M., Kallas, E. G., Souza, R. F. & Holmes, E. C. (1996) Genetics 153, 1077-1089.
27. Leitner, T., Kumar, S. & Albert, J. (1997) J. Virol. 71, 4761-4770.
28. Schröder, E. (1870) Z. Math. Phys. 15, 361-376.
29. Felsenstein, J. (1981) J. Mol. Evol. 17, 368-376.
30. Abramowitz, M. & Stegun, I. A. (1912) Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables (Dover, New York).
31. Stanton, D. & White, D. (1986) Constructive Combinatorics (Springer, New York).
32. Huelsenbeck, J. P. & Dyer, K. A. (2004) J. Mol. Evol. 58, 661-672.
33. Ferguson, T. S. (1973) Ann. Stat. 1, 209-230.
34. Antoniak, C. E. (1974) Ann. Stat. 2, 1152-1174.
35. Ewens, W. J. & Tavaré, S. (1998) in Encyclopedia of Statistical Science, eds. Kotz, S., Read, C. B. & Banks, D. L. (Wiley, New York), pp. 230-234.
36. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953) J. Chem. Phys. 21, 1087-1092.
37. Hastings, W. K. (1970) Biometrika 57, 97-109.
38. Tierney, L. (1996) in Markov Chain Monte Carlo in Practice, eds. Gilks, W. R., Richardson, S. & Spiegelhalter, D. J. (Chapman & Hall, New York), pp. 59-74.
39. Larget, B. & Simon, D. L. (1999) Mol. Biol. Evol. 16, 750-759.
40. Neal, R. M. (2000) J. Comput. Graph. Stat. 9, 249-265.