# list.seqs

The list.seqs command will write out the names of the sequences found within a fastq, fasta, name, group, count, list, or align.report file. This could be useful for using the get.seqs and remove.seqs commands as well as to generate a group file. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.

## Options

At least one of the following options must be used. Each of these options will generate a file ending in accnos that contains a single column containing the list of the sequences contained in the input file.

### fastq option

The fastq option is used as presented in the following command:

mothur > list.seqs(fastq=test.fastq)


### fasta option

The fasta option is used as presented in the following command:

mothur > list.seqs(fasta=esophagus.fasta)


The resulting esophagus.accnos file looks something like:

59_10_1
59_10_10
59_10_11
59_10_13
59_10_15
59_10_16
59_10_17
...


### name option

The name option is used as presented in the following command (be sure to run unique.seqs on esophagus.fasta first):

mothur > list.seqs(name=esophagus.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. It can also contain group information.

mothur > list.seqs(count=esophagus.count_table)


### group option

The group option is used as presented in the following command:

mothur > list.seqs(group=esophagus.groups)


### alignreport option

The alignreport option is used as presented in the following command:

mothur > list.seqs(alignreport=esophagus.align.report)


### list option

The list option is used as presented in the following command:

mothur > list.seqs(list=esophagus.fn.list)


### taxonomy option

The taxonomy option is used as presented in the following command:

mothur > list.seqs(taxonomy=esophagus.silva.full.taxonomy)