The command reads a fasta file or series of fasta files and creates a group file.

Default Options

mothur >, groups=A-B-C)

This command will generate a .group file that looks like:

sample1Seq!   A
sample1Seq2   A
sample1Seq3   A
sample1Seq4   A
sample1Seq5   A
sample2Seq!   B
sample2Seq2   B
sample2Seq3   B
sample2Seq4   B
sample2Seq5   B
sample3Seq!   C
sample3Seq2   C
sample3Seq3   C
sample3Seq4   C
sample3Seq5   C


The output parameter allows you to specify the name of group file or count file created.


The format parameter allows you to specify whether the outputted file is a group file or count file. Options group or count. Default=count.


  • 1.38.1 Fixes bug with output directory
  • 1.40.0 Bug Fix: Adds deliminator to output file for multiple groups. mergegroups -> merge.groups. #384
  • 1.42.0 Bug Fix: Fixes output filename for #602
  • 1.48.0 Adds format parameter