I’m confused about the default sorting of the get.oturep command. Is it simply OTU1, 2, 3, etc…? Isn’t that what the sorted=name option is for? I just want to make sure I fully understand the command before I use data from it for phylogenetic trees.
By default, mothur prints the OTU reps in the order the OTUs are in the list file. You can order the representatives in the fasta file using the sort option. Choices are name, bin, size and group. Name is the representative name. Bin is the OTULabel. (This is most likely the default unless you have manually altered your list file to reorder the OTUs). Size is the abundance of the OTU. Group is the groups represented in the OTU.