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%									  %
%	Multiple Sequence Alignment by Parallel Simulated Annealing 	  %
%	 								  %
%	 	1992.7 Check and refine every program 			  %
%		for IFS (ICOT Free Software) release.			  %
%	 								  %
%	(C)1992 Institute for New Generation Computer Technology 	  %
%	$BG[I[!"$=$NB>$O(BCOPYRIGHT$B%U%!%$%k$r;2>H$7$F2<$5$$!#(B		  %
% 	(Read COPYRIGHT for detail information.) 			  %
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README$B!J(BEnglish Version$B!K(B

1:Abstract

Multiple sequence alignment problem can be considered as a
combinatorial optimization problem. Simulated Annealing is
one of the effective algorithm for such a problem.

The parallelized simulated annealing algorithm developed at ICOT can
be executed without temperature scheduling which is the most difficult
problem in convetional simulated annealing.

This program is an application of the parallelized simulated annealing
for multiple sequence alignment problem, and produces the real
multiple sequence alignment, implemented on PIM(with 64 Processing Elements)
written in KL1 language.

2:Environment

	Machine : PIM/m or Multi-PSI $B!J(B64PE$B!K(B

	SIMPOS  : Version A20 (PSI/UX) 

	PIMOS   : PIMOS/ CAL/ CSP/   KL1/   KL0/ParaG
	Version	   3400/0192/0103/014800/001500/3200

3:Files

#####################################################################
KL1 Source File     # Save File     # Module Name   # Unload File   #
#####################################################################
--------------------------------------------------------------------|
cp1.kl1             |               | cp            |               |
------------------------------------|---------------|               |
dayhoff3.kl1        | dayhoff3.sav  | dayhoff       |               |
------------------------------------|---------------|               |
energy3.kl1         |               | energy        |               |
------------------------------------|---------------|               |
etable3_1.kl1 	    |               | energy_table  |               |
------------------------------------|---------------|               |
exp1.kl1            | exp1.sav      | exp_new       |   sa3_1.exe   |
------------------------------------|---------------|               |
io3.kl1             |               | io            |               |
------------------------------------|---------------|               |
move_io3_1.kl1      |               | move          |               |
------------------------------------|---------------|		    |
input3.kl1          |               | input         |               |
------------------------------------|---------------|		    |
sa3_1.kl1           |               | sa            |               |
---------------------------------------------------------------------
#####################################################################
ESP Source File     #  Simpos Package Name  #			    #
#####################################################################
--------------------------------------------------------------------|
dna1c.esp	    |   user	  	    |			    |
---------------------------------------------------------------------
#####################################################################
Unload File(Object)#  Relink Modules         			    #
#####################################################################
--------------------------------------------------------------------|
sa3_1.exe	   | [energy_table,dayhoff,energy,exp_new,move,cp,  |
		   |  io,input,sa]				    |
---------------------------------------------------------------------
#####################################################################
Other File     |						    #
#####################################################################
--------------------------------------------------------------------|
README	       |  README in English	                            |
--------------------------------------------------------------------|
README.j       |  README in Japanese	                            |
--------------------------------------------------------------------|
INSTALL	       |  How to install in English	                    |
--------------------------------------------------------------------|
INSTALL.j      |  How to install in Japanese	                    |
--------------------------------------------------------------------|
setup.com      |  Command file for SETUP	                    |
--------------------------------------------------------------------|
DOC	       |  Document (explanation of this software)           |
--------------------------------------------------------------------|
DEMO	       |  How to DEMO in English	                    |
--------------------------------------------------------------------|
DEMO.j	       |  How to DEMO in Japanese	                    |
---------------------------------------------------------------------

4:Install
	Copy Files.
	On SIMPOS,catalogue ESP program, and save it.
	Read INSTALL for further information.

5:Demonstration
	On PIMOS, take setup.com.
	In listener,
		?- sa.[return]
	appearing left window,
		START> [return]

	Read DEMO for further information.


