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:

Instead of:

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.