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src/q/i/qiime-1.8.0/qiime/make_phylogeny.py   qiime(Download)
#app controllers that implement align_unaligned_seqs
import cogent.app.muscle_v38
import cogent.app.clustalw
import cogent.app.mafft
import cogent.app.raxml_v730

src/q/i/qiime-1.8.0/qiime/align_seqs.py   qiime(Download)
from cogent.app.infernal import cmalign_from_alignment
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence
import cogent.app.clustalw
import cogent.app.mafft