The fungal region (ITS) is not alignable so I am using pairwise.seqs to get a distance matrix… I know I will get a .dist file that can be used in the cluster command however does this command also produce a .list file? In make.shared, remove.rare, and get.oturep commands all need a .list file. If pairwise.seqs does not produce a .list file how can I make a .shared file, get OTU reps, etc?
THANK YOU!
Cheers
Yes, cluster produces a list http://www.mothur.org/wiki/List_file, rabund http://www.mothur.org/wiki/Rabund_file and sabund http://www.mothur.org/wiki/Sabund_file file. Here’s a link to Pat’s example analysis, http://www.mothur.org/wiki/Schloss_SOP. It highlights many of mothur’s commands. Also, some helpful wiki links, 
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http://www.mothur.org/wiki/Make.shared
http://www.mothur.org/wiki/Mothur_manual
http://www.mothur.org/wiki/Frequently_asked_questions
http://www.mothur.org/wiki/Silva_reference_files
http://www.mothur.org/wiki/MiSeq_SOP
Most Awesome thank you!.. Now to wait 4 mores days for pairwiase.seqs to run! Ha!