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Align.check (version
You can also provide a name file associated with your fasta file
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

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 align.check command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs.