The merge.count command will combine multiple count table files and output the result to a new file.

To run the merge.count command you need to provide the input files separated by hyphens as well as the name file that the contents of those files should be written to. The merging occurs in the order that you provide the input files. The following example demonstrates how to use the command:

mothur > merge.count(count=fileA-fileB-fileC, output=fileABC)

NOTE: You cannot merge.count files with group information with files that do not include group information. Data would be lost.


  • 1.38.1 - First Introduced
  • 1.42.0 - Merge.count command ignores duplicate names. #259