The sort.seqs command puts sequences from a fasta, name, count, group, quality, flow or taxonomy file in the same order.


The command will generate a *.sorted.* file. You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.

accnos option

To use the accnos option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta)

name option

To use the name option, follow this example:

mothur > sort.seqs(fasta=GQY1XT001.shhh.trim.unique.align, name=GQY1XT001.shhh.trim.names)

count option

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence.

mothur > sort.seqs(fasta=GQY1XT001.shhh.trim.unique.align, count=GQY1XT001.shhh.trim.count_table)

group option

To use the group option, follow this example:

mothur > sort.seqs(accnos=order.accnos, group=GQY1XT001.shhh.groups)

fasta option

To use the fasta option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta)

flow option

To use the flow option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, flow=GQY1XT001.shhh.trim.flow)

taxonomy option

To use the taxonomy option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.fasta, taxonomy=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy)

qfile option

To use the qfile option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, qfile=GQY1XT001.shhh.trim.qual)


The large parameter indicates your files are too large to fit in RAM, default=F.

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, qfile=GQY1XT001.shhh.trim.qual, large=T)


  • 1.24.0 - First introduced.
  • 1.28.0 - Added count option
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350