请教
我想计算序列的基因距离，按照文献的方法就是要做“distance by phylogenetic analysis"，文献中方法说：the synonmous (Ds) and non-synonymous (Da) nucleotide p-distances were calculated by MEGA program using the Nei-Gojobori methods. The synonymous versus non-synonymous ratio (Ds/Da) were also calculated.那么，我在计算时，substitution model中，substitutions to include->应该选择哪个呢（分别有1、s:synonymous only; 2、N:nonsynonymous only; 3、difference s-n; 4、difference n-s; 5、S: No. of synonymous sites；6、N: No. of nonsynonymous sites）？
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