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The get.rabund command will generate an rabund file based on the OTU data that you have read into mothur.
If you read in a list file, get.rabund will generate the corresponding rabund file:
mothur > read.otu(list=amazon.fn.list) mothur > get.rabund()
This series of commands will generate amazon.fn.rabund.
If the list file contains multiple lines and you are only interested in a subset of those lines you can use the label option:
mothur > get.rabund(label=unique-0.03-0.10-0.20)
By default the data in the rabund file are not sorted. That is they are in the same order as the OTUs in your list file. If you would like these data to be sorted by their abundance you need to use the sorted option:
mothur > get.rabund(sorted=T)