
Using nhmmer is essentially the same as hmmsearch, with a number of
additional flags:

% hmmbuild model_file.hmm alignment.file
% nhmmer model_file.hmm target_db.fasta
% nhmmer -h     //  gives you a list of available flags

//example run:
% hmmbuild SNORD96_test.hmm tutorial/SNORD96.sto
% nhmmer -o SNORD96_test.out SNORD96_test.hmm tutorial/dna_target.fa

By default, nhmmer searches both the sequence in the target database
and its reverse complement.

More complete documentation is in the works. This version should be 
treated as an early beta. If you run into any questions/problems 
along the way, please let us know.

