Get.oturep command requires distance marice, list file and a fasta file. Have I understood correctly that mothur uses distance matrice and the list file to identify the representative seq? And that the fasta file is only used for getting those sequences? So that fasta file is not used in distance calculations anymore at that stage?
THe reason I am asking this is that I have generated my distance matrice in a another program using amino acid sequences and in running the get.oturep I have my sequences as nucleotides. THis is because I have noticed that no matter what command you run in mothur with amino acid sequences they are just full of N:s afterwards.
University of JyvÃ¤skylÃ¤