NOTE: Starting with mothur version 1.18.0 the read.otu command no longer exists. You can enter your file names directly into the commands that use them. For example:
mothur > read.otu(list=98_sq_phylip_amazon.fn.list) mothur > collect.single()
you would run:
mothur > collect.single(list=98_sq_phylip_amazon.fn.list)
To make a shared file from a list and group file mothur now has a new command make.shared.