Hi,
Is it possible to use .shared file for classify.seqs?
No, but perhaps you are looking for the classify.otu command, http://www.mothur.org/wiki/Classify.otu. It requires a list file.
Thanks for your reply. I am trying to make sub samples of my data to normalise them and use them for further classification! I used make.shar for sub sampling, but i have no idea how to proceed further!
You would want to subsample the list, taxonomy, names and group files. Then run the make.shared command.
mothur > sub.sample(list=yourListFile, taxonomy=yourTaxonomyfile, name=yourNameFile, group=yourGroupFile, persample=t)
mothur > make.shared(list=current, group=current) - create a shared file from your subsampled dataset
mothur > classify.otu(list=current, group=current, taxonomy=current, name=current) - classify subsampled otus.
But really, there is no reason to subsample the taxonomy data since the consensus taxonomy won’t change