Diversity Estimates

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Hi same person:

I am wondering about your diversity estimates. How exactly did you calculate these? Are they just averages across the four nucleotides from the table output of deviaTE? It isn't stated in the supplemental materials as far as I can find.

Copynumber I understand, as normalized to a single gene. But as far as divergence, do you suggest isolating consensus sequences from the alignments to the library then building a tree from these?

Thank you for getting back to me. I really appreciate your help.

Christopher