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The get.sabund command will generate an sabund file based on the OTU data that you have read into mothur. For example, if you read in a list file, get.rabund will generate the corresponding sabund file:
mothur > read.otu(list=amazon.fn.list) mothur > get.sabund()
This series of commands will generate amazon.fn.sabund. If the list file contains multiple lines and you are only interested in a subset of those line you can use the label option:
mothur > get.sabund(label=unique-0.03-0.10-0.20)