HMMER v2.3.2 must be installed on the same system as EMBOSS and the location of the HMMER executables must be defined in your path for EMBASSY HMMER to work.

Where possible the same command line qualifier names and parameter order is used as in the original HMMER. There are however several unavoidable differences and these are clearly documented.

More or less all options documented as "expert" in the original HMMER user guide are given in ACD as "advanced" options. -options must be specified on the command line to be prompted for a value for them.

The original HMMER uses the BLAST environment variables, if defined, to locate files whereas the EMBASSY HMMER does not.

Input and output of alignments and sequences is limited to the formats that the original HMMER supports. It would be fairly straightforward to adapt the code to support all EMBOSS-supported formats.

Automatic processing of gzip files is not supported.

HMMER v2.3.2 and therefore EMBASSY HMMER is only recommended for use with protein sequences. If you provide a non-protein sequence you will be reprompted for a protein sequence - this is achieved by setting the type: attribute of sequence inputs to protein in the ACD file. To accept nucleic acid sequences you'll need to replace protein with nucleic.