The group file is used to assign sequences to a specific group. It consists of 2 columns separated by a tab. The first column contains the sequence name. The second column contains the group name. Here is an example:
AY457915 A AY457914 A AY457913 A AY457912 A AY457911 A AY457910 A AY457909 A AY457908 A AY457907 A AY457906 A ...
1. Be sure not to include the “>” in the name of the sequence.
2. You sequence name and group name cannot contain blank spaces. For example, the following will cause an error: AY457915 Dirt Sample
3. DO NOT use a hyphen in group names. The “-“ character is used within mothur to separate group names, labels, taxonomies, ect. Including a hyphen will cause issues in your downstream analysis.