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In this paper, based on molecular clock hypothesis and the amino acid mutations Dayhoff the probability matrix model, using a computer program to simulate randomly generated from the initial start of the mutant protein sequence of evolutionary process, and data collection simulation experiments, the use of statistical methods of data processing and analysis. Thus, our ancestors were drawn between the sequence of evolutionary sequence, random divergence between the two homologous sequence of amino acid mutations and the consistency of the model. At the same time homologous sequence of the difference between an acceptable rate of mutation, and the relationship between the different sites to estimate the mutation rate in the case of distribution subject to the shape parameters, the ancestral sequence and evolution of sequence between 2.25 and The random divergence between the two homologous sequence compared with 1.9.