These steps are optional, and will only apply (I think) to sufficiently POSIX-compliant operating systems like UNIX, Linux, or WinNT.
HMMER reads four environment variables, and is designed to coexist peacefully with an installation of WUBLAST or NCBI BLAST:
If you have installed BLAST, you probably already have the two BLAST environment variables set in system-wide or user-specific .cshrc files.
All four variables are optional. If they are set up, you can simplify
command lines to:
> hmmpfam pfam my.query
> hmmsearch my.hmm swiss35
> hmmpfam /some/long/path/to/databases/pfam my.query
> hmmsearch my.hmm /some/long/path/to/databases/swiss35