Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

@article{Yang2004MaximumLP,
  title={Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods},
  author={Z. Yang},
  journal={Journal of Molecular Evolution},
  year={2004},
  volume={39},
  pages={306-314}
}
  • Z. Yang
  • Published 2004
  • Biology, Medicine
  • Journal of Molecular Evolution
  • Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the “discrete gamma model,” uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates… CONTINUE READING
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    References

    SHOWING 1-10 OF 41 REFERENCES
    Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.
    • Z. Yang
    • Biology, Medicine
    • Molecular biology and evolution
    • 1993
    • 967
    • Highly Influential
    Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
    • 431
    • PDF
    Estimating the pattern of nucleotide substitution
    • Z. Yang
    • Biology, Medicine
    • Journal of Molecular Evolution
    • 2004
    • 854
    • PDF
    Evolutionary trees from DNA sequences: A maximum likelihood approach
    • 11,188
    • Highly Influential
    • PDF
    Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
    • J. Wakeley
    • Biology, Medicine
    • Journal of Molecular Evolution
    • 2004
    • 266
    • PDF
    Mixed model analysis of DNA sequence evolution.
    • 48
    Limitations of the evolutionary parsimony method of phylogenetic analysis.
    • L. Jin, M. Nei
    • Biology, Medicine
    • Molecular biology and evolution
    • 1990
    • 383
    • PDF
    Toward a more accurate time scale for the human mitochondrial DNA tree
    • 181
    Rates of molecular evolution and the fraction of nucleotide positions free to vary
    • S. Palumbi
    • Biology, Medicine
    • Journal of Molecular Evolution
    • 2005
    • 25