ITS data using mothur

I have used mothur for 16SRNA as well as 18SRNA data analysis, in which the only difference is the the use of silva database only when doing 18SRNA. However, now that I am doing ITS data, i understand that i need to print out a table for each 3 phylum and carry 3 different analysis. My only problem is that I am new to mothur and do not quiet understand where to change the mothur commands to print out the 3 different tables. Any help in that regard will be appreciated.

Thank you,


you can use the UNITE2 database which is already formatted correctly here

Thanks Kendra! so basically the difference between these three data types is the database we use for the alignment?
16S:greengenes, SILVA, RDP
let em know if that corrects. Thanks again!

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