This is our first attempt for a software package for 
	Detecting Conserved RNA Structures 
by combining thermodynamic prediction with an multiple sequence alignment.
This software is part of the Vienna RNA Package, see
http://www.tbi.univie.ac.at/~ivo/RNA/


In general typing
     make all
should be sufficient to build the three programs alidot, pfrali and amount.
We also provide several helpful perl scripts (see below). You may have to 
adjust the path to your perl in the first line of these scripts.

You really should read the Manual (in info, html or dvi format). However,
for the impatient, here's a short synopsis:

The programs alidot, pfrali and amount read alignments from stdin, e.g. as:
  alidot < clustal.aln
where clustal.aln contains a CLUSTAL W alignment. For each sequence name
in the alignment file there must be a .mfe file in the current directory
for alidot and a _dp.ps file for pfrali and amount.

amount produces aligned mountain plots suitable for input to xmgr;
n+2 sets will be produces the last two being the average and mean distance.

Output of alidot and pfrali: 
a) to stdout the list of base pairs sorted by 
   number of incompatible sequences, number of compensatory mutations,
   and frequency or pseudo-entropy 
b) a file aln_dp.ps/aln_pf_dp.ps containing the color coded dot plot
   red    only one type of base pair (no compensatory mutations)
   ochre  2 types
   green  3 types
   pale   some sequence are non-compatible
   Only base pairs compatible with all higher ranked pairs are shown 
   on the lower left side.
Look at colors.ps for an example of the color code.

Perl scripts:
dpzoom.pl: zoom into a dot plot,
	   e.g. dpzoom.pl -f 100 -l 300 aln_dp.ps > aln_100-300.ps
consens.pl: produce consensus sequence and structure,
	   e.g. consens.pl seqs.aln alidot.out > consens
cmount.pl: produced colored mountain representation from aln_dp.ps
split.pl:  split RNAfold output with many structures into individual .mfe files
xrna.pl:   annotate Xrna plots
anote.pl:  annotate structure plots from RNAplot

AliDot.pl: A perl Tk application to view the output of alidot and pfrali.
	Better than looking at the postscript dot-plots in gv. Use as e.g.:
		AliDot.pl alidot.out	
	Requires perl 5.004 or later with Tk extensions.


WARNING: This not (yet) stable software. Please do not redistribute this
version and use at your own risk.

Send comments and bugs reports to 
ivo@tbi.univie.ac.at