REFCOMP README


1)	refcomp beta 
        Refcomp is a computer program which determines single base pair  
	mismatching sites betweeen a defined reference sequence and a 
	consensus sequence generated by an assembly of sequences.
	
2)	Platforms
	
	DEC-Alpha
	HP-UX
	SGI
	Solaris
	SunOS

3)	Packing list

	refcomp
	README
	EXAMPLE.DOC
	INSTALL
	REFCOMP.DOC
        ./example/chromat_dir/*
        ./example/edit_dir/*
        ./example/phd_dir/*
        ./example/poly_dir/*
	./perl/phredPhrapRef


4)	In order to run refcomp you will need

	phred 0.961028 or later
        phd2seqfasta 0.960108 or later
        phd2qualfasta 0.960108 or later
	phrap 0.960731 or later
	consed 4.0
	phredPhrap

	For phred, phd2seqfasta, and phd2qualfasta  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 refcomp distribution e-mail as a text file named 
	'refcomp.email'


6)	Decode the text file by typing 'uudecode refcomp.email'


7)	Unpack the distribution by typing 'zcat refcomp.tar.Z | tar xfv -'


8)	Change directory to 'refcomp' by typing 'cd refcomp'


9)	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.


10)	Directions for installing refcomp are provided in INSTALL.


11)	An introduction and more detailed description of refcomp is available
	in REFCOMP.DOC.