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  • Title: [Evaluation and extension of Markov process models for the evolution of DNA].
    Author: Yang Z, Goldman N.
    Journal: Yi Chuan Xue Bao; 1994; 21(1):17-23. PubMed ID: 8003346.
    Abstract:
    Markov process models of nucleotide substitution are evaluated. A model proposed by Lanave et al (1984), alleged to need no priori assumption about the substitution pattern, is found to have the assumption of reversibility. Calculations based on the 2-p, 4-p, and 6-p substitution schemes show that site variation of substitution speed leads to serious under-estimation of sequence divergence by various methods. Spatial pattern variation also leads to under-estimation, but the discrepancy is slight. A nonhomogeneous Markov process model is used to study the temporal variations of rates and it is shown that the estimated number of substitutions reflects a rate averaged over time. The implications of those results to evolutionary phylogenetics are discussed.
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