Codon-substitution models for heterogeneous selection pressure at amino acid sites.
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Summary
Development of models that account for heterogeneous omega ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences are developed, useful for testing for adaptive molecular evolution and identifying amino Acid sites under diversifying selection.
- Type
- article
- Published
- 2000-04-29
- Cited by
- 2,370
- References
- 46
- Access
- Open access
- OpenAlex
- https://openalex.org/W2160364329
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1757552
Keywords
Nonsynonymous substitution, Biology, Synonymous substitution, Negative selection, Genetics
References
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- PAML: a program package for phylogenetic analysis by maximum likelihood
- The neutral theory of molecular evolution
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- Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
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- Long term trends in the evolution of H(3) HA1 human influenza type A.
- A codon-based model designed to describe lentiviral evolution.
- HIV-1 regulatory/accessory genes: keys to unraveling viral and host cell biology.
- Population dynamics of flaviviruses revealed by molecular phylogenies.
- Episodic adaptive evolution of primate lysozymes
- Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders
- In search of molecular darwinism
- The neutral theory of molecular evolution.
- Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions
- Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees.
- Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
- Statistical tests of neutrality in the age of weak selection.
- Coalescing into the 21st century: An overview and prospects of coalescent theory.
- Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts.
Cited by
- The analysis of genes expressed in the sperm storage organs of Drosophila melanogaster: Patterns of evolution and expression
- The neutral theory in the genomic era.
- Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.
- A novel use of equilibrium frequencies in models of sequence evolution.
- Molecular Characteristics of Human Immunodeficiency Virus Type 1 Subtype C Viruses from KwaZulu-Natal, South Africa: Implications for Vaccine and Antiretroviral Control Strategies
- Genetic and antigenic analysis of two recently circulating genotypes of type A foot-and-mouth disease virus in India: evidence for positive selection in the capsid-coding genes
- Potential impact of recombination on sitewise approaches for detecting positive natural selection.
- A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.
- A simple hierarchical approach to modeling distributions of substitution rates.
- Molecular Evolution and Phylogeny of Sipunculan Hemerythrins
- Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato).
- Identifying sites under positive selection with uncertain parameter estimates.
- A Bayesian perspective on a non-parsimonious parsimony model.
- Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
- Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma
- The defensin gene family expansion in the tick Ixodes scapularis.
- Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic
- Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco
- Evolution of adaptive phenotypic traits without positive Darwinian selection
- Evolution of MHC class I genes in the European badger (Meles meles)
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