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Pcr.seqs (version 1.39.5.0)

fasta - Candiate Sequences:

sequences must be aligned

Trim with an oligos file?:

oligos - barcodes and primers:

a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file.

nomatch - action when no primer is found:

keepprimer - keep the primer in the output sequence:

keepdots - keep the leading and trailing alignment dots in the output sequences:

taxonomy - Sequence Taxonomy:

name - Sequence representative name list:

group - Group file:

pdiffs - number of differences to allow in the forward primers (default 0):

rdiffs - number of differences to allow in the reverse primers (default 0):

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The pcr.seqs command assigns sequences to chosen taxonomy outline.