Simple and accurate estimation of ancestral protein sequences

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

Volumn 103, Issue 14, 2006, Pages 5431-5436

  Hall, Barry G ^a  

^a Bellingham Research Institute   (United States)

Author keywords

Ancestral state; Bayesian; Phylogenetics

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; COMPUTER SIMULATION; EVOLUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

BASE SEQUENCE; BAYES THEOREM; COMPUTER SIMULATION; DNA; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEINS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 33645790071     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0508991103     Document Type: Article

References (29)

1. Chandrasekharan, U. M., Sanker, S., Glynias, M. J., Karnik, S. S. & Husain, A. (1996) Science 271, 502-505.
2. Zhang, J. & Rosenberg, H. F. (2002) Proc. Natl. Acad. Sci. USA 99, 5486-5491.
3. Golding, G. B. & Dean, A. M. (1998) Mol. Biol. Evol. 15, 355-369.
4. Gaucher, E. A., Thomson, J. M., Burgan, M. F. & Benner, S. A. (2003) Nature 425, 285-288.
5. Chang, B. S., Jonsson, K., Kazmi, M. A., Donoghue, M. J. & Sakmar, T. P. (2002) Mol. Biol. Evol. 19, 1483-1489.
6. Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F. & Wilson, A. C. (1990) Nature 345, 86-89.
7. Chang, A. C. & Cohen, S. N. (1978) J. Bacteriol. 134, 1141-1156.
8. Thomson, J. M., Gaucher, E. A., Burgan, M. F., De Kee, D. W., Li, T., Aris, J. P. & Benner, S. A. (2005) Nat. Genet. 37, 630-635.
9. Jermann, T. M., Opitz, J. G., Stackhouse, J. & Benner, S. A. (1995) Nature 374, 57-59.
10. Nambiar, K. P., Stackhouse, J., Stauffer, D. M., Kennedy, W. P., Eldredge, J. K. & Benner, S. A. (1984) Science 223, 1299-1301.
11. Stackhouse, J., Presnell, S. R., McGeehan, G. M., Nambiar, K. P. & Benner, S. A. (1990) FEBS Lett. 262, 104-106.
12. Felsenstein, J. (2004) PHYLIP (Phylogeny Inference Package) (Department Genome of Sciences, Univ. of Washington, Seattle).
13. Swofford, D. L. (1993) PAUP: Phylogenetic Analysis Using Parsimony (Illinois Natural History Survey, Champaign, IL).
14. Swofford, D. L. (2000) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) (Sinauer Associates, Sunderland, MA).
15. Pupko, T., Pe'er, I., Shamir, R. & Graur, D. (2000) Mol. Biol. Evol. 17, 890-896.
16. Yang, Z. (1997) Comput. Appl. Biosci. 13, 555-556.
17. Zhang, J. & Nei, M. (1997) J. Mol. Evol. 44, Suppl. 1, S139-S146.
18. Koshi, J. M. & Goldstein, R. A. (1996) J. Mol. Evol. 42, 313-320.
19. Cai, W., Pei, J. & Grishin, N. V. (2004) BMC Evol. Biol. 4, 33.
20. Ronquist, F. & Huelsenbeck, J. P. (2003) Bioinformatics 19, 1572-1574.
21. Hall, B. G. (2005) Mol. Biol. Evol. 22, 792-802.
22. Hall, B. G. (2004) Phylogenetic Trees Made Easy: A How-To Manual (Sinauer Associates, Sunderland, MA).
23. Barlow, M. & Hall, B. G. (2002) J. Mol. Evol. 55, 314-321.
24. Hall, B. G. (2004) CODONALIGN (Bellingham Research Institute, Bellingham, WA).
25. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997) Nucleic Acids Res. 25, 4876-4882.
26. Maddison, W. P. & Maddison, D. R. (1992) MACCLADE: Analysis of Phylogeny and Character Evolution (Sinauer Associates, Sunderland, MA).
27. Felsenstein, J. (1981) J. Mol. Evol. 17, 368-376.
28. Huelsenbeck, J. P. & Ronquist, F. (2001) Bioinformatics 17, 754-755.
29. Tatusova, T. A. & Madden, T. L. (1999) FEMS Microbiol. Lett. 174, 247-250.