I am new in using MOTHUR and this far I managed to cope using the well written manual.
I am working with a protein coding gene and trying to compare cloning libraries. I have 200 DNA and 200 infered amino-acid sequences. I aligned them using DNAdist and PROTdist of PHYLIP and introduced them to MOTHUR to create OTUs. Firstly I wanted to create OTUs grouping only identical sequences. I used the “cluster” command of MOTHUR and then “get.oturep” with “label=unique”. For the DNA panel I got 150 OTUs and 200 OTUs for the protein panel (the same DNA sequence would give different amino-acid sequence?).
I chose 2 DNA OTUs each grouping 3 sequences, checked the distance matrix and aligned them using CLustalW, sequences from each OTU were really identical. I did the same with their infered amino acid sequences => also 100 % similar. Why doesn’t MOTHUR group identical amino acid sequences in the same OTU?
Thank you for help