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bin.seqs prints out a fasta-formatted file where sequences are ordered according to the OTU that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. For this tutorial, download and decompress AmazonData.zip.

Default settings

To execute the bin.seqs() you must provide a list file and the fasta option must be used to provide a fasta-formatted file that has the sequences represented in the list file.

mothur > bin.seqs(list=98_sq_phylip_amazon.an.list, fasta=amazon.fasta)

This command will generate 12 fasta-formatted files. Each file represents a different label. Within each file the sequences are sorted according to the OTU that they belong to. The sequence names have been modified to indicate its OTU grouping. For example, the file 98_sq_phylip_amazon.an.0.10.fasta contains the following output:

>U68686	Otu01
>U68635	Otu01
>U68610	Otu04

The number indicates the OTU that the sequence belongs to.



If you provide a group file, then in addition to the OTU number the group will also be provided.

>U68589	forest	Otu01
>U68590	forest	Otu02
>U68591	forest	Otu03
>U68687	pasture	Otu04
>U68592	forest	Otu04


A names file indicating sequence names that are identical to a references sequence, may be inputted to bin.seqs so that the fasta and list files are complementary. The following commands illustrate this:

mothur > bin.seqs(list=98_sq_phylip_amazon.an.list, fasta=amazon.unique.fasta, name=amazon.names)


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. If you ran the cluster command with a count file, be sure to include the count file with this command as the list file will only contain the unique names.

mothur > bin.seqs(list=final.an.unique_list.list, fasta=final.fasta, count=final.count_table, label=0.03)
>GQY1XT001EH8KN	F003D000-F003D142-F003D144-F003D146-F003D150	Otu0001	NumRep=41
>GQY1XT001CRCO3	F003D004	Otu0001	NumRep=1
>GQY1XT001C0JER	F003D146	Otu0001	NumRep=1
>GQY1XT001APSXD	F003D142-F003D144	Otu0001	NumRep=4


There may only be a couple of lines in your OTU data that you are interested in running through bin.seqs(). There are two options. You could: (i) manually delete the lines you aren't interested in from your list file; (ii) or use the label option. If you only want to read in the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:

mothur >  bin.seqs(list=98_sq_phylip_amazon.an.list, fasta=amazon.fasta, label=unique-0.03-0.05-0.10)


  • 1.28.0 Added count parameter