#######################
###    Introduction
#######################
This document is intended to help users to effectively (1) setup and (2) run ld_compare. 

Before you begin compiling or running ld_compare please make sure
that you have read the README and downloaded all necessary files:
	(1) README.txt
	(2) User Manual
	(3) Precompiled binaries for
		Microsoft Windows (32-bit)
		Linux on i386
		Linux on amd64
		Sun Microsystems Solaris
	(4) src directory stores the source code and MakeFile
	(5) sample parameter and input files 


#######################
###    Installation
#######################
If there is a precompiled binary for your architechture go ahead and use it.  If
not then go to the src directory and use the command "make" to compile.  The
binary will be made in the bin directory in a subdirectory for your
architechture.


#######################
###    Working Examples
#######################
Under ./examples/, sample input files are provided to illustrate both single-
and multiple-marker coverage.

(1) On Microsoft windows
	ld_compare.exe examples\Multiple_Marker\hap_Chr24.par
        ld_compare.exe examples\Single_Marker\par.txt

(2) On unix-like operating systems
	ld_compare examples/Multiple_Marker/hap_Chr24_linux.par
        ld_compare examples/Single_Marker/par_linux.txt


Now you are ready to use LDCompare. If you still have problems, check your
directory and file permissions and read user manual and README file.

Have fun and please report back any feedback and suggestions.

Dr. Ke Hao (ke_hao@affymetrix.com)
05/03/2006
