What commands can i use?

This is the first time in my life I will be using mothur analysis. I have several aligned Raoultell sequences. What commands can be useful in obtaining a heat map or a rarefaction curve?

Thank you in advance for your answer.

Welcome! It sounds like you need to check out the MiSeq SOP. You might also want to see my minimalR materials for analyzing output from mothur in R

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