First, many thanks for the continuous improvements of Mothur. Recently, I had some problems for routinely handle some files.
Is there a simple way to make a .groups file when you have a lot of fastas (more than 400 in my case). I understand that the make.group function is useful when you have thousands of sequences in few fastas but It is not convenient for many fastas. Maybe it is silly but would it be possible to add the option of making a .groups file when using the merge.files function. The same kind of problem occurred with the merge.files function, it is not convenient writing the names of 400 fasta files to merge them. I generally use a simple command line in linux that detect all .fasta files in a directory and merge them, is it feasible with Mothur?
Thank you in advance for your answer
So how do you have 400 fastas with out barcodes or something you can run through trim.seqs? Regardless, you can always write a perl/python script to make your own group file. We show how to do this in the very old now Sogin data analysis wiki page.