• Publications
  • Influence
Codon-substitution models for heterogeneous selection pressure at amino acid sites.
TLDR
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. Expand
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
TLDR
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. Expand
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
  • Z. Yang
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 May 1998
TLDR
The likelihood analysis confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages. Expand
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.
TLDR
Two codon-based models for the evolution of protein-coding DNA sequences account for varying selection intensity among amino acid sites and are applied to a data set of the V3 region of the HIV-1 envelope gene, providing strong support for variable selection intensity. Expand
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
TLDR
An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree, which has a probability of approximately 95%. Expand
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
TLDR
A new approximate method is proposed that takes into account two major features of DNA sequence evolution: transition/transversion rate bias and base/codon frequency bias and is superior to earlier approximate methods and may be useful for analyzing large data sets, although maximum likelihood appears to always be the method of choice. Expand
Among-site rate variation and its impact on phylogenetic analyses.
  • Z. Yang
  • Biology, Medicine
  • Trends in ecology & evolution
  • 1 September 1996
TLDR
Analysis of reliable methods for studying rate variation shows that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies. Expand
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.
  • Z. Yang
  • Biology, Medicine
  • Molecular biology and evolution
  • 1 November 1993
TLDR
Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences is extended to the case where substitution rates over sites are described by the gamma distribution and a numerical example is presented to show that the method fits the data better than do previous models. Expand
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.
TLDR
Computer simulation is used to investigate the accuracy and power of the likelihood ratio test (LRT) in detecting positive selection at amino acid sites and it is found that use of the chi(2) distribution makes the test conservative, especially when the data contain very short and highly similar sequences. Expand
A new method of inference of ancestral nucleotide and amino acid sequences.
TLDR
A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species, and the new likelihood-based method was found to be superior to the parsimony method. Expand
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