All files in these directories are covered by the SUPERFAMILY license
agreement at http://supfam.org/SUPERFAMILY/license.html.
Only users covered by a valid license may download files.
Please visit http://supfam.org/SUPERFAMILY/downloads.html for
more information.

There is some documentation describing how to install and use the 
scripts with the HMMs here: 
http://supfam.org/SUPERFAMILY/howto_use_models.html

The ass3.pl script is highly recommended.  It should be
used to generate consistent assignments from the output files from HMM
scoring on a sequence database.
The superfamily.pl script is a wrapper that should run all the others.
The ass_to_html.pl scripts should convert the ass file output to HTML for human viewing.
The hmmscan.pl wrapper script is one that threads HMMER3 more efficiently than its native threading.
The fasta_checker.pl script should be run on any database before scoring
with HMMs.  Pipe the standard output to a file to get the cleaned fasta
file.  Errors will be reported to standard error.
The a2m2selex.pl file converts the SAM 'a2m' format into the HMMER 'selex'
format.  This is useful for building HMMER models with the -hand option.
The familyassignment.pl script includes family level classification, but 
requires SCOP parseable files which are downloadable from the SCOP website 
(http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html).

MD5SUMs
df0ca45b2f59499e93f8c0265a60e331  a2m2selex.pl
c20880edb393c46a117bf52e24376fed  fasta_checker.pl
12b03bbb1943ce5388a6dc9e2ad01ab0  hmmscan.pl
d81a302bc93c13fd921b114e99e97470  superfamily.pl
1034fa675989631fcdf3c27cb86e8a85  ass_to_html.pl
2e6e1e63b17fb3b8a5cb7595514383d1  ass3.pl
