HMMER - profile hidden Markov models for biological sequence analysis
Version 2.0 (June 1998)
Copyright (C) 1992-1998 Washington University School of Medicine

HMMER is freely distributed under the GNU General Public License (GPL).
See the file COPYING for information on HMMER's free license.
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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
   In short: after uncompressing and un-tar'ing the distribution,
   type "make" in the top level directory if you're on any UNIX system.
   For more detailed instructions, see INSTALL.
   You should also read the following files:

   COPYING      -- copyright notice, and information on the free software license
   GNULICENSE   -- Full text of the GNU Public License, version 2 (see COPYING)
   NOTES        -- Release notes


o Quick start (...to hell with the documentation...)
   A quick intro is given in NOTES, using some demo files in the Demos/
   subdirectory.

o Slow start (ok, where's the documentation?)
   The User's Guide is in Userguide/Userguide.ps [Postscript, 59 pages].
   It is also available online as hypertext:
	http://hmmer.wustl.edu/hmmer-html/ 

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
Dept. of Genetics 
Washington University School of Medicine, St. Louis, Missouri, USA
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