QRNA - Comparative analysis of biological sequences 
       with pair hidden Markov models, pair stochastic context-free
       grammars, and probabilistic evolutionary  models.
     
Version 2.0.3d (FEB 2006)
Copyright (C) 2000-2006 Howard Hughes Medical Institute/Washington University School of Medicine
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o About this software...
   QRNA is an implementation of pair-HMM and pair-SCFG methods
   to extract probablistic inference from comparative analysis
   about the functionality of a conserved region.

   Basically, you give QRNA an alignment of two DNA sequences as input 
   (alignment produced with BLASTN or any other method);
   it basically looks at the alignment and statistically
   tests  (based on the observed pattern of mutation) whether it's more
   likely to come from a coding exon, a structural RNA, or something
   else. 

o Getting QRNA
   WWW home:       http://selab.wustl.edu/cgi-bin/selab.pl?mode=software
   Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/software/

o Installing QRNA
   See the file INSTALL for brief 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)

 Getting started with QRNA
   The User's Guide is in documents/userguide.ps [PostScript]. 


o Reporting bugs
   These programs are under active development.  If
   you use these programs, please help me out and e-mail me with
   suggestions, comments, and bug reports. (elena@genetics.wustl.edu)

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