Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences

Molecular Biology and Evolution

Volumn 23, Issue 1, 2006, Pages 7-9

  Shapiro, Beth ^a   Rambaut, Andrew ^a   Drummond, Alexei J ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Phylogenetic inference; Protein coding sequences; Substitution models

Indexed keywords

NUCLEOTIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CODON; COST; MODEL; PHYLOGENY; RNA VIRUS; STATISTICAL ANALYSIS; VIRUS; YEAST;

CLASSIFICATION; CODON; MODELS, GENETIC; PHYLOGENY; PROTEINS; RNA VIRUSES; SEQUENCE ALIGNMENT; YEASTS;

RNA VIRUSES;

EID: 28944450584     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj021     Document Type: Article

References (22)

1. Bruno, W. J., and A. L. Halpern. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
2. Buckley, T. R., and C. W. Cunningham. 2002. The effects of nucleotide substitution models assumptions on estimates of nonparametric bootstrap support. Mol. Biol. Evol. 19:394-405.
3. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
4. _. 2001. The troubled growth of statistical phylogenetics. Syst. Biol. 50:465-467.
5. Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
6. Goldman, N., and Z. H. Yang. 1994. A codon-based model of nucleotide substitution for protein coding DNA sequences. Mol. Biol. Evol. 11:725-736.
7. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
8. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
9. Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20:86-93.
10. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
11. Penny, D., P. J. Lockhart, M. A. Steel, and M. D. Hendy. 1994. The role of models in reconstructing evolutionary trees. Pp. 211-230 in R. W. Scotland, D. J. Siebert, and D. M. Williams, eds. Models in phylogenetic reconstruction. Clarendon Press, Oxford.
12. Posada, D. 2001. The effect of branch length variation on the selection of models in molecular evolution. J. Mol. Evol. 52:434-444.
13. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808.
14. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
15. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
16. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
17. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
18. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
19. _. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.
20. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
21. Yang, Z. H. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
22. Yang, Z. H., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.