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How saturated are the sequences in four fold degenerate sites? Mentioning this would be important to get a feeling on the level of good information in the sequences£¨4±¶¼ò²¢Î»µãÊÇÈçºÎ´ïµ½±¥ºÍµÄ£©.

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I don't know what you are working on. If you used nucleotide coding sequences to address some synonymous substitution issues, you should consider the saturation effect of synonymous or four fold degenerate sites. The nucleotide divergence at four fold degenerate sites between two lineages will increase with time since the latest common ancestor, up to some saturation level. Hence, if two potein coding sequences are less similar, the distance based on synonymous changes may not account for its actual divergence. Therefore, you should be catious of this issue when you analyze your data.
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