I’m adding data to an ongoing project. I used to do this easily by cat fasta/name/group after removing chimeras but now I’m using count_tables rather than name/group. How do you merge 2 count tables?
Mothur does not have a direct way to do this, but it’s a good feature request! Here’s a workaround in the meantime:
mothur > deunique.seqs(fasta=yourFastaFileDataSet1, count=yourCountFileDataSet1) - creates fasta and group file
mothur > deunique.seqs(fasta=yourFastaFileDataSet2, count=yourCountFileDataSet2) - creates fasta and group file
mothur > merge.files(input=redundantFastaFile1-redundantFastaFile2, output=fullFastaFile) - combine fasta files
mothur > merge.files(input=redundantGroupFile1-redundantGroupFile2, output=fullGroupFile) - combine group files
mothur > unique.seqs(fasta=fullFastaFile) - deconvolute fasta file and generate name file
mothur > count.seqs(name=nameFileFromUniqueSeqs, group=fullGroupFile) - create new count table
Thanks for the work around!
Merge.count command coming for 1.39.0 
The merge.count command is part of 1.38.1, https://github.com/mothur/mothur/releases/tag/v1.38.1.1.