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

Default Options

mothur > make.group(fasta=sample1.fasta-sample2.fasta-sample3.fasta, 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


  • 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 make.group. #602