I was reading the split.abund wiki page but wasn’t clear what each output file is. I ran split.abund using a fasta and count table file with cutoff=1 (pull out singletons) and accnos=true. Do the .rare. files mean they only list samples with singletons and the .abund. files list everything else except singletons?

Yes if cutoff=1, then the *rare files contain OTUs with 1 sequence and the *abund files contain OTUs with more than one sequence.

Awesome, thanks!