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#dist.seqs
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# dist.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/dist.seqs, tempdefault=./TestReferences)
set.logfile(name=distseqs.logfile)
dist.seqs(fasta=dist.fasta, calc=jtt, cutoff=0.05)
dist.seqs(fasta=dist.fasta, calc=pmb, cutoff=0.03)
dist.seqs(fasta=dist.fasta, calc=pam, cutoff=0.03)
dist.seqs(fasta=dist.fasta, calc=kimura, cutoff=0.03)
dist.seqs(fasta=dist.fasta, calc=onegap, cutoff=0.03)
dist.seqs(fasta=dist.fasta, calc=nogaps, cutoff=0.10)
dist.seqs(fasta=dist.fasta, calc=eachgap, cutoff=0.15)
quit()
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