How to calculate nucleotide diversity among different genes within a secondary metabolite gene cluster, across different strains of the same species?

10 October 2020 0 7K Report

I am working on different secondary metabolite gene clusters from different strains of the same species. With a reference genome for comparison, I have found out putative sequences for some genes under each cluster, from each of the strains. Now I want to find out the sequence diversity among those strains, w.r.t the gene sequences, for individual clusters. How should I go about it? Thanks in advance for the suggestions that'lll be coming along.

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