HMMER - profile hidden Markov models for biological sequence analysis
Version 2.2 (August 2001)
Copyright (C) 1992-2001 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.wustl.edu/
   Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/

o Installing HMMER
   See the file INSTALL for brief instructions.
   See the chapter Installation in the HMMER User's Guide for more 
   detailed instructions.

   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
   The User's Guide is in Userguide/Userguide.pdf [Adobe PDF format]. 
   It is also available online as hypertext:
	http://hmmer.wustl.edu/hmmer-html/ 

   A quick tutorial intro is given as the first chapter of
   the User's Guide.

o Registering HMMER
   Email eddy@genetics.wustl.edu to register and get on my
   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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