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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
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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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