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.sabund will generate the corresponding sabund file:
mothur > get.sabund(list=amazon.fn.list)
mothur > get.sabund(rabund=amazon.fn.rabund)
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(list=amazon.fn.list, label=unique-0.03-0.10-0.20)
If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file with the get.sabund command.
mothur > get.sabund(list=amazon.an.unique_list, count=amazon.count_table)
- 1.31.0 - Added count parameter.