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#align.seqs
# testAlign is stability.trim.contigs.good.unique.fasta from MiSeq_SOP
# test different align method and seaches
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
set.dir(input=./TestFiles, output=./TestResults/align.seqs, tempdefault=./TestReferences)
set.logfile(name=alignseqs.logfile)
align.seqs(fasta=testAlign.fasta, reference=silva.v4.fasta)
summary.seqs(fasta=current)
align.seqs(fasta=testAlign.fasta, reference=silva.v4.fasta, align=needleman)
summary.seqs(fasta=current)
align.seqs(fasta=testAlign.fasta, reference=silva.v4.fasta, align=gotoh)
summary.seqs(fasta=current)
quit()
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