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******************************** RecPars ******************************************
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Author:		Kim Fisker

The program is currently maintained by:

                Thomas Christensen
		Department of Computer Science
		University of Aarhus
                Ny Munkegade, Bldg. 540
                DK-8000 Aarhus C, Denmark
                phone: +45 89 3236

Copying:	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 1, or (at your option)
    		any later version.


Description:	RecPars does a parsimony analysis of DNA sequences. It tries to find
		the best phylogenies for different regions of the sequences and
		thereby postulating a recombination event between these segments.
		A more thoroughly explanation can be found in:
		
		J. Hein. "A Heuristic Method to Reconstruct the History of Sequences
                subject to Recombination.", Journal of Molecular Evolution, 36:
		396--406, 1993.

		K. Fisker and J. Hein. "Reconstructing a Simulated History of
		Sequences Subject to Recombination.", Not publiced yet.


Installation:	Customize the Makefile to your environment -- It should be very easy.
		Type 'make' and the program 'RecPars' should be ready.


How to use:	 RecPars  -p <parameterfile>  [-o <outputfile>]
		
	<parameterfile>: 
		         substfile = HIV-subst
			 datafile = HIV-align
			 debug = yes
			 rekombcost = 100
			 initial_phyl = best 0 100
			 rounds = 3

			 'substfile' is a file with substitution costs. It should have
			 the following format:

					    A  C   G   T   -
					A   0  1   1   1   1
					C   1  0   1   1   1
					G   1  1   0   1   1
					T   1  1   1   0   1
					-   1  1   1   1   0

			 'datafile' contains the aligned DNA sequences. It should have
			 the following format:

					% '%' is the comment sign.
					% it start with the number of sequences and
					% their length
					4 11

					% sequence 1
					AACT
					TT__
					GGC 

					% sequence 2
					AACT
					TT__
					GGC 

					% sequence 3
					AACT
					TT__
					GGC 

					% sequence 4
					AACT
					TT__
					GGC 

			 'debug' = yes or no. yes gives a little more information.
			 Default value is yes.

			 'recombcost' is the cost of a recombination event in the
			 parsimony analysis. Default value is 100. Should be customized
			 to the actual sequences.

			 'initial_phyl' tells what segment in the sequences that should 
			 be used when finding the initial phylogeny. Default is the first
			 100 positions (best 0 100).

			 'rounds' is the number of parses over the sequences performed.
			 Default value is 2 and means that the sequences are scanned
			 first forward and then backward.

			 'only_one_phyl' = yes or no. If set to yes RecPars only finds
			 the best phylogeny for the segment pointed to by 'initial_phyl'
			 and then returns. Default value is no.


Results:		Example outputfile: Comments indicated by ^^^^

			SUBSTFILE = /users/kfisker/rekomb/simulation/data/subst
			DATAFILE = /users/kfisker/rekomb/simulation/sim/fileali
			DEBUG = YES
			REKOMBCOST = 10
			INITIAL PHYLOGENI = BEST 0 100
			ROUNDS = 1
			ONLY_ONE_PHYL = NO
			^^^^ first the given parameters
			Minimal Tree cost = 543
			^^^^ sum of necessary substitution costs in every position
			Removed positions has cost = 200
			^^^^ RecPars ignores non-informative positions
			Read 11 sequences with length 1000
			Removed all positions(columns) with 11 or 10 equal bases
			^^^^ definition of non-informative positions
			Remaining bases in each sequence = 408
			^^^^ number of informative positions left.
			Tree 1: start = 1 , end = 443 , cost = 349 , rekomb = 1
			^^^^ first phylogeny covers position 1 to 443


			        |------------------------ 6
			    |---|                            
			    |   |------------------------ 8
			 ---|                                
			    |                       |---- 4
			    |                   |---|        
			    |                   |   |---- 10
			    |               |---|            
			    |               |   |-------- 0
			    |           |---|                
			    |           |   |------------ 9
			    |       |---|                    
			    |       |   |   |------------ 5
			    |       |   |---|                
			    |       |       |------------ 2
			    |   |---|                        
			    |   |   |-------------------- 7
			    |---|                            
			        |   |-------------------- 3
			        |---|                        
			            |-------------------- 1
			^^^^ sequences are numbered according to position in the inputfile.
			^^^^ CAUTION: The root is placed arbitrarily

			Tree 2: start = 450 , end = 999 , cost = 253 , rekomb = 0

			        |------------------------ 6
			    |---|                            
			    |   |------------------------ 8
			 ---|                                
			    |           |---------------- 5
			    |       |---|                    
			    |       |   |---------------- 2
			    |   |---|                        
			    |   |   |               |---- 4
			    |   |   |           |---|        
			    |   |   |           |   |---- 10
			    |   |   |       |---|            
			    |   |   |       |   |-------- 0
			    |   |   |   |---|                
			    |   |   |   |   |------------ 9
			    |   |   |---|                    
			    |   |       |---------------- 7
			    |---|                            
			        |   |-------------------- 3
			        |---|                        
			            |-------------------- 1


			Total Cost = 612
			^^^^ total cost of entire solution