-----------------------------------------------------------------------
  ********************
  ***** KalignP ******
  ********************
  KalignP version 1.0 by Nanjiang Shu 2010
  Department of Biochemistry and Biophysics 
  Stockholm University
  nanjiang@sbc.su.se

  Description: multiple sequence alignment supporting external supplied
  position specific gap penalties

  This software is derived from 
  Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
  http://msa.cgb.ki.se/
  timolassmann@gmail.com

	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.
-----------------------------------------------------------------------
Installation:

% ./configure 
% make

and as root:

% make install

Compiler:

It is recommenced to use the Intel compiler 'icc' to compile kalignP which increase the speed by about 15%.
To enable the icc compiler, change the line in the Makefile
"CC					= gcc  "
to 
"CC					= icc  "

and rerun the compilation by the command
% make -B


Usage:

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

        Options:
        
	type: kalignP -h 
	

-----------------------------------------------------------------------

=====================================================================
Updated 2011-01-19 by Nanjiang Shu, nanjiang@sbc.su.se
