HMMER - profile hidden Markov models for biological sequence analysis
Version 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
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o About this software...
   HMMER is an implementation of profile HMM methods for
   sensitive database searches using multiple sequence alignments as queries.

   Basically, you give HMMER a multiple sequence alignment as input;
   it builds a statistical model called a "hidden Markov model"
   which you can then use as a query into a sequence database
   to find (and/or align) additional homologues of the sequence family.


o Getting HMMER
   WWW home:       http://hmmer.janelia.org/
   Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
   User's Guide:   ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf


o Installing HMMER
   See the file INSTALL for brief instructions.
   See the chapter Installation in the HMMER User's Guide (Userguide.pdf)
   for more detailed instructions.
   See the file NOTES for notes particular to this release.

   You should also read the following files:
   COPYING   -- copyright notice, and information on the free software license
   LICENSE   -- Full text of the GNU Public License, version 2 (see COPYING)
 
   If you have obtained HMMER from Washington University under
   a non-GPL license as part of a special licensing agreement,
   COPYING and LICENSE will refer to the terms of that agreement.


o Getting started with HMMER
   See the Tutorial section of the User's Guide (Userguide.pdf)
   for a quick introduction to how to use HMMER.


o Registering HMMER
   Email eddy@genetics.wustl.edu to register and get on my
   very infrequent mailing list of HMMER news, patches, and updates.


o Reporting bugs
   These programs are under active development. Though this
   release has been tested and appears to be stable, bugs may crop up. If
   you use these programs, please help me out and e-mail me with
   suggestions, comments, and bug reports. (eddy@genetics.wustl.edu)

   
Sean Eddy
Howard Hughes Medical Institute and Dept. of Genetics 
Washington University School of Medicine, St. Louis, Missouri, USA
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