REFCOMP INSTALLATION INSTRUCTIONS


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
	SGI
	Solaris
	SunOS

3) 	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 4.1
	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)

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

5)	Edit phredPhrapRef.  The variable '$binDir' should be set to the 
	name of the directory where refcomp and  phredPhrap will be
	installed.
	The variable '$aceFile' should be set to the name of the ace file
        produced when phredPhrap is run on your system.

6)	Copy  ./perl/phredPhrapRef,  
	to a directory on your system where executables are stored.

7)	Run RefComp on your own data  For more information regarding
	RefComp execution and the expected directory structure used to
	organize input and output files please refer to EXAMPLE.DOC and 
	REFCOMP.doc.