MEME data table of NOD-1 in Ungulates

We ran a meme analysis using datamonkey to find sites that have undergone episodic positive selection. Here, the alpha value represents the dS, or rate of synonymous substitution. dN, the rate of non-synonymous substitutions, is represented by two variables: beta plus and beta minus. The sites are under positive selection when beta positive is greater than alpha. Statistical significance is calculated using the likelihood ratio test. Our p value was calculated to be 0.1.
After finding the sites of positive selection we used the locations of domains annotated by HMMR scan to label each site of diversifying selection’s respective domain. Sites of positive selection in unannotated domains were excluded from our data. Overall, we found that there were 18 sites of positive selection in the NOD-1 domain, 6 sites of positive selection in LRR domains, and 3 sites of positive selection in the CARD domain.