*                                                                             *
*  Program: RefComp                                                           *
*  Version: 2.0                                                               *
*  Copyright (C) 1998                                                         *
*  by Deborah A. Nickerson,  Natali Kolker, Scott Taylor,  and Mark Rieder    *
*  University of Washington                                                   *
*                                                                             *
*  All rights reserved.                                                       *
*                                                                             *
*  This software is part of a beta-test version of the Refcomp                *
*  distribution package.  It may not be redistributed, distributed            *
*  in modified form, or used for any commercial purpose, including            *
*  commercially funded sequencing, without written permission from            *
*  the authors and the University of Washington.                              *
*                                                                             *
*  This software is provided ``AS IS'' and any express or implied             *
*  warranties, including, but not limited to, the implied warranties of       *
*  merchantability and fitness for a particular purpose are disclaimed.       *
*  In particular, this disclaimer applies to any diagnostic purpose. In no    *
*  event shall the authors or the University of Washington be liable for      *
*  any direct, indirect, incidental, special, exemplary, or consequential     *
*  damages (including, but not limited to, procurement of substitute goods    *
*  or services; loss of use, data, or profits; or business interruption)      *
*  however caused and on any theory of liability, whether in contract,        *
*  strict liability, or tort (including negligence or otherwise) arising      *
*  in any way out of the use of this software, even if advised of the         *
*  possibility of such damage.                                                *
*                                                                             *


1)	Make sure consed 4.0 or 5.0 is installed on your system.

2)	Type 'cd example/edit_dir'

3) 	Type 'consed'

4)	Select the ace file 'example.fasta.ace' and the contig 'Contig1'.
5) 	The aligned reads window pops up.  Make sure that the color mode
	is 'Color means quality and tags'.

6)	Mismatches are tagged with the 'polymorphism' tag 
	(default color is slate blue).

7)	Go to the 'Navigate' menu and select 'Tags'.  Select 'polymorphism'
	to navigate by polymorphism tag.

8)	Hit 'Go' to advance the aligned reads to the position of the first
	putative heterozygote.  Use 'Prev' and 'Next' to navigate by 

9)	Examples of real mismatches
        are at unpadded positions: 87, 772, 2756, 4101, 4317.
	Notice :
	Each mismatch site has been tagged if quality value in corresponding
        consensus sequence  position is above Phrap quality 20.

10)	Click on a read and base of interest with the second mouse button
	to view the sequence data.

11)	Quit consed.


1)	Install refcomp(see README and INSTALL)

2)	Create the following directory structure in your working directory


3)	Move your chromats into 'chromat_dir'

4)	Change directory into 'edit_dir'

4)	Type 'phredPhrapRef [basename]' 
        phredPhrap [basename] and after that refcomp.

5)	Run consed.