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HMMER reads three optional environment variables:
  HMMERDB  - directory location of HMM databases (e.g. PFAM)
  BLASTDB  - directory location of FASTA-formatted sequence databases
  BLASTMAT - directory location of PAM scoring matrices

The BLASTDB and BLASTMAT variables are shared with versions of BLAST such
as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port).  If these
variables are set, you do not have to specify the full path to your
databases on the command line when using HMMER.

Please see the documentation for more information.
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