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.
The seq.error command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment. This is demonstrated in https://mothur.org/wiki/miseq_sop/#assessing-error-rates