The unique.seqs command returns only the unique sequences found in a fasta-formatted sequence file and a file that indicates those sequences that are identical to the reference sequence. Often times a collection of sequences will have a significant number of identical sequences. It sucks up considerable processing time to have to align, calculate distances, and cluster each of these sequences individually. For this tutorial, you should use the files found in the amazondata.zip archive.

To run the command the name of a fasta-file needs to be provided:

mothur > unique.seqs(fasta=amazon.fasta)

This will generate two files: amazon.names and amazon.unique.fasta. You can now align amazon.unique.fasta and generate a distance matrix. Then you can use that matrix with the newly generated amazon.name file with the names option for the cluster command.

name option

If you align your unique sequences, filter and screen them, you might be removing bases from the sequences that accounted for differences between the sequences. You can then rerun your sequences through unique.seqs by providing a name file for the name option:

mothur > unique.seqs(fasta=amazon.unique.filter.fasta, name=amazon.names)

When redundant sequences are found, the list of names corresponding to the sequence names will be merged.


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. It can also contain group information.

mothur > unique.seqs(fasta=amazon.unique.filter.fasta, count=amazon.count_table)

When redundant sequences are found, the counts corresponding to the sequences will be added.


The format parameter is used to indicate what type of file you want outputted. Choices are name and count, default=name unless count file used then default=count.

mothur > unique.seqs(fasta=amazon.fasta, format=count)


  • 1.22.0 Name file prints in same order as fasta file.
  • 1.28.0 Added count parameter
  • 1.31.1 Bug Fix: segfault with count file containing group info.
  • 1.37.0 Adds format parameter #125