get.oturep after cluster.split


I have got a problem in obtaining representative fasta-files. Maybe I just miss something and there is a simple way around it. Since the distance file would exceed my memory, I switches -as recommended- to the cluster.split by taxonomy method. Everything works perfect, however, for downstream analysis I would like to extract representative DNA-sequences for each OTU. get.oturep usually does the job, but it requires a .dist file, which is of course not present when you choose to work with cluster.split.

Is there a way around it, e.g. with get.sharedseq or is there a way for get.oturep to split a distance file similar to cluster.split?

Thanks a lot!

Try using method=abundance

Thanks a lot, that was easy :slight_smile: