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?



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Yes, cluster produces a list, rabund and sabund file. Here’s a link to Pat’s example analysis, It highlights many of mothur’s commands. Also, some helpful wiki links, :smiley: .

Most Awesome thank you!.. Now to wait 4 mores days for pairwiase.seqs to run! Ha! :smiley: