#pairwise.seqs
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# pairwise.fasta is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta from MiSeq_SOP
#
# test different classification methods and seaches
set.dir(input=./TestFiles, output=./TestResults/pairwise.seqs, tempdefault=./TestReferences)
set.logfile(name=pairwiseseqs.logfile)
pairwise.seqs(fasta=pairwise.fasta, kmercutoff=-0.5, cutoff=0.05)
pairwise.seqs(fasta=pairwise.fasta, calc=onegap, cutoff=0.03)
pairwise.seqs(fasta=pairwise.fasta, calc=nogaps, cutoff=0.10)
pairwise.seqs(fasta=pairwise.fasta, calc=eachgap, cutoff=0.15)
quit()

