out rep seq without distance


Is there a way to get representative sequence names for specific OTUs without the need of the distance matrix as required for the get.oturep command?


You can get the representative sequences based on abundance rather than distance (i.e. the most common sequence in the OTU is the representative). That just requires your fasta and list file, no need for distance. You just need to specify the method as ‘abundance’ (the default is ‘distance’):

mothur > get.oturep(fasta=XXX, count=XXX, list=XXX, method=abundance)

I don’t think you can specify exact OTUs at that step, but it’s a very quick one to perform and you get easy extract your OTUs of interest afterwards.

Awesome! Thanks! :smiley: