POLYPHRED-3.5 README

1)	Polyphred 3.5

	Polyphred is a computer program which identifies putative 
	heterozygotes for single nucleotide substitution polymorphisms 
	in fluorescence-based DNA sequence traces.  

2)	Platforms
	
	DEC-Alpha
        Linux
	SGI
	Solaris
	SunOS

3)	Packing list

	polyphred
	README
	EXAMPLE.doc
	INSTALL
	POLYPHRED.doc
	POLYTOOL.doc
        ./example/chromat_dir/*
        ./example/edit_dir/*
        ./example/phd_dir/*
        ./example/poly_dir/*
	


4)	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)


5)	Save the README and Polyphred attachments to files. 
	Create a directory called Polyphred ('mkdir Polyphred') and move the
	saved attachments into the new directory ('mv README ./Polyphred' and
	'mv polyphred.tar.gz ./Polyphred'). 


6)	Change directories into the new Polyphred directory ('cd Polyphred').
	Unpack the Polyphred distribution by typing 'gunzip polyphred.tar.gz'
	followed by 'tar xvf polyphred.tar'


7)	The example can be viewed as soon as its been unpacked if consed 4.1
	is already installed on your system.  It is recommended that you first
	look at the example and then try your own data.  Please refer to 
	EXAMPLE.DOC.


8)	Directions for installing polyphred are provided in INSTALL.


9)	An introduction and more detailed description of polyphred is available
	in POLYPHRED.DOC.