Retrieve top n hits from reference template file

Hello everyone,

I wish to retrieve top 5 hits from the 16S reference files (greengenes, silva) along with my querry sequences. The align.seqs command returns only the aligned user provided sequences.
How do I get the top “n” sequences?


You’d need to run a blast script from the command line. This isn’t part of mothur. If you wanted the consensus classification from those five, you could do classify.seqs, method=blast or method=distance and knn=5.