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PAML 4: phylogenetic analysis by maximum likelihood.
  • Ziheng Yang
  • Medicine, Biology
  • Molecular biology and evolution
  • 1 August 2007
TLDR
PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Expand
PAML: a program package for phylogenetic analysis by maximum likelihood
  • Ziheng Yang
  • Computer Science, Medicine
  • Comput. Appl. Biosci.
  • 1 October 1997
TLDR
The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models, which include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Expand
Bayes empirical bayes inference of amino acid sites under positive selection.
TLDR
A Bayes empirical Bayes (BEB) approach to the Codon-based substitution models problem is developed, which assigns a prior to the model parameters and integrates over their uncertainties, and the results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach. Expand
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
  • Ziheng Yang
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 1 September 1994
TLDR
Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites, and one of them uses several categories of rates to approximate the gamma distribution, with equal probability for each category. Expand
Bayesian species delimitation using multilocus sequence data
TLDR
A Bayesian modeling approach is used to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations. Expand
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.
TLDR
A modified branch-site model is described and used to construct two LRTs, one of which is a direct test of positive selection on the lineages of interest and is recommended for use in real data analysis and the other appears robust against violations of model assumptions. Expand
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
TLDR
The results of the method are found to be insensitive to changes in the rate parameter of the branching process, and the best trees estimated by the new method are the same as those from the maximum likelihood analysis of separate topologies, but the posterior probabilities are quite different from the bootstrap proportions. Expand
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
TLDR
A Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes is developed and applied to published noncoding DNA sequences from the human and the great apes. Expand
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
TLDR
Previous models to allow the omega ratio to vary both among sites and among lineages and implement the new models in the likelihood framework are extended and may be useful for identifying positive selection along prespecified lineages that affects only a few sites in the protein. Expand
Estimating the pattern of nucleotide substitution
  • Ziheng Yang
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 1 July 1994
TLDR
It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. Expand
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