POLYPHRED-3.5 INSTALLATION NOTES

1)	Polyphred 3.5 

	Polyphred is an application which identifies putative heterozygotes 
	for substitution SNPs in fluorescence-based DNA sequence traces.  

2)	Platforms

	DEC-Alpha
	Linux
	SGI
	Solaris
	SunOS
	
3) 	In order to run Polyphred you will need

	Phred 0.961028 or later
        Phd2fasta 0.971024 or later
	Phrap 0.960731 or later
	Consed 8.0 or later
	PhredPhrap

	For Phred, Phd2fasta   contact 
	Brent Ewing (bge@u.washington.edu)

	For Phrap contact
	Phil Green (phg@u.washington.edu)

	For Consed and PhredPhrap contact
	David Gordon (gordon@genome.washington.edu)

4)	Make sure the required software is installed on your system.

5)      Edit phredPhrap:

	Uncomment the following line:
        	$polyPhredExe = "/usr/local/genome/bin/polyphred";
        
	Change the 0 to 1 
        	$bUsingPolyPhred = 1;

6)      You can also run PolyTool, which is a graphical 
	interface for running PolyPhred see (POLYTOOL.doc).
         

7)      In order to see polyPhred tags in Consed the contents of
	POLYPHRED.CONSEDRC  (included with this distribution in 
	given path) need to be added to the appropriate .consedrc file.  
	Consed resources can be specified in three different ways, in 
	a file named .consedrc in the top level of a user home directory 
	(user specific consed resources), in a file named .consedrc in
	the edit_dir of project (project specific consed resources), and 
	in a file named by the environment variable CONSED_PARAMETERS 
	(system wide consed resources).  For more information about consed
	resources see the section named CONSED CUSTOMIZATION in the consed
	documentation.