Can we use mothur for 23S analysis?

Hi All,
Can we do 23S analysis with mothur just like we do for 16S? If yes, What reference files are to be used?

You can, but you’ll need to find reference files for the analysis as there aren’t any supported/hosted by the mothur team (I think…).

SILVA is a good place to to go. That have an aligned and taxonomically assigned 23S rRNA database (LSU releases). You would need to export out the sequences of interest and taxonomies using ARB, but then you should be good to go.