hmmbuild [options] hmmfile alignfile

Options

-f

Configure the model for finding multiple domains per sequence, where each domain can be a local (fragmentary) alignment.

-g

Configure the model for finding a single global alignment to a target sequence.

-h

Print brief help.

-n s

Name this HMM s.

-o f

Re-save the starting alignment to f, in Stockholm format.

-s

Configure the model for finding a single local alignment per target sequence.

-A

Append this model to an existing hmmfile rather than creating hmmfile.

-F

Force overwriting of an existing hmmfile.