hmmpfam [options] hmmfile seqfile
Print brief help.
Specify that models and sequence are nucleic acid, not protein.
Limits the alignment output to the n best scoring domains.
Set the E-value cutoff for the per-sequence ranked hit list to x, where x is a positive real number.
Set the bit score cutoff for the per-sequence ranked hit list to x, where x is a real number.
Calculate the E-value scores as if we had seen a sequence database of n sequences.