Problems to generate make.shared.file

Hi all,

Hopefully somebody can help me. I’m not totally new to mothur as I analyzed most of my single microbial communities with it. But now I want to compare these communities with each other in a multiple sample analyses, and I`m already failing to generate the make.shared.file.
I have three communities to compare (A-B-C). When I’m establishing the group file should I use the command and the three single unique.fasta files for community A, B and C, and if yes, how should I generate the needed single list.file for the make.shared command? In case, that I 'm barking up the wrong tree, can anybody support me with I short tutorial which files I should use for generating the list and group file for multiple sample analyses?

Sorry to bother you with that, but I already spend a serious amount of time to find out myself.



You have to start with all of the sequences together in one fasta file and one group file and then go from there.