The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Abstract
A codon-based model for the evolution of protein-coding DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.
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“The first codon models estimated parameters representing an averaged nonsynonymous-synonymous rate ratio.”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Goldman and Yang 1994
Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei, M., & Gojobori, T. (1986) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040410 · Cited by 4,904
The Theory of Stochastic Processes
Cox, D. R., Miller, H. D., Weiss, G., & Shuler, K. (1966) · Physics Today · doi:10.1063/1.3047872 · Cited by 3,324
Amino Acid Difference Formula to Help Explain Protein Evolution
Grantham, R. L. (1974) · Science · doi:10.1126/science.185.4154.862 · Cited by 2,363
Mitochondrial DNA sequences of primates: tempo and mode of evolution
Brown, W. M., Prager, E. M., Wang, A., & Wilson, A. C. (1982) · Journal of Molecular Evolution · doi:10.1007/bf01734101 · Cited by 1,554
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
Li, W. (1993) · Journal of Molecular Evolution · doi:10.1007/bf02407308 · Cited by 1,088
Estimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076
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Items 1,001–1,002 of 1,002
Shi, L., Hu, E., Wang, Z., Liu, J., Li, J., Li, M., Chen, H., Yu, C., Jiang, T., & Su, B. (2017) · Human Genetics · doi:10.1007/s00439-016-1748-5 · Cited by 20
Goto, H., Watanabe, K., Araragi, N., Kageyama, R., Tanaka, K., Kuroki, Y., Toyoda, A., Hattori, M., Sakaki, Y., Fujiyama, A., et al. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-224 · Cited by 16
Metadata
- Authors
- Goldman, N., & Yang, Z.
- Affiliations
- National Institute for Medical Research (GB)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1994-09
- Volume
- 11
- Issue
- 5
- Pages
- 725-36
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W1920973730
- Cited by
- 1,960
- References
- 31
- Citations by year
- 2026: 18 · 2025: 42 · 2024: 51 · 2023: 43 · 2022: 61 · 2021: 65 · 2020: 60 · 2019: 74 · 2018: 71 · 2017: 60 · 2016: 69 · 2015: 68 · 2014: 107 · 2013: 97 · 2012: 89
- FWCI
- 2.27
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Eye Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- Markov processes, codon usage bias, selective constraint, synonymous substitution rate, nonsynonymous substitution rate, phylogenetic estimation, nucleotide substitution models
- MeSH terms
- Animals, Chemistry, Physical, Codon, DNA, Genes, Globins, Mammals, Markov Chains, Models, Genetic, Nucleotidyltransferases, Phylogeny, Proteins, Likelihood Functions, Point Mutation, Glucose-1-Phosphate Adenylyltransferase, Chemical Phenomena
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