./download.sh:
./download.sh <url_of_HMMER_binaries>
OUTPUT:
Creates a ./HMMER/ and keeps all binaries into it
./pfamdb.sh
OUTPUT:
Dwnlds pfam-A dbase and creates an index of all .hmm files
./pfamFinder.sh
scans for Pfam-A domains in the query file and provides 2 outputs (output1 and output3) of different formatting styles.