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  Kalign version 1.03, Copyright (C) 2004, 2005 Timo Lassmann

  http://msa.cgb.ki.se/
  timo.lassmann@cgb.ki.se

	This program is free software; you can redistribute it and/or modify
	it under the terms of the GNU General Public License as published by
	the Free Software Foundation; either version 2 of the License, or
	any later version.

	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of
	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
	GNU General Public License for more details.

	You should have received a copy of the GNU General Public License
	along with this program; if not, write to the Free Software
	Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  
	A copy of this license is in the COPYING file.
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Installation:

%make

and as root:

%make install


Usage:
        kalign [Options]  infile.fasta outfile.fasta
        or:
        kalign [Options] -i infile.fasta -o outfile.fasta
        or:
        kalign [Options] < infile.fasta > outfile.fasta

        Options:
        -i/-input       Name of input file.
        -o/-output      Name of output file.
        -gpo/-gap_open  Gap open penalty (default 6.0).
        -gpe/gap_ext    Gap extension penalty (default 0.9).
        -p/-points      Wu-Manber algorithm used in both distance calculation and dynamic programming
        -w              Wu-Manber algorithm not used at all
        -f/-fast        fast heuristic alignment
                        ( - recommended for >500 sequences)

        -q              'quiet' - no messages are sent to standard error

        Without an option specified Kalign will use the Wu-Manber algorithm for distance calculation only.
                ( - recommended for < 500 sequences)

Revision History:

Kalign 1.02:

	- introduced -q (for 'quiet') option -> nothing is written to stderr
	 
Kalign 1.01: 

	- input alignment can be read from stdin and output printed to stdout
	
	i.e. to run kalign:
		
	kalign < input_alignment.fasta > output_alignment.fasta [options]
	
Kalign 1.0:

	initial release of Kalign
	
	