Note: These instructions are meant for Linux on the 
CS dept computers. 

Where to download the programs
------------------------------

ms:

http://home.uchicago.edu/~rhudson1/source/mksamples.html

	Click on "LINK" and download ms.tar and msdoc.pdf

	The documentation will be very useful when using
	the program.

COSI:

http://www.broadinstitute.org/~sfs/cosi/
	
	Download cosi_1.1.tar


Compiling ms
------------

Let's assume you have ms.tar on your desktop. Then, type
in the terminal:

	cd ~/Desktop
	tar xf ms.tar
	cd msdir
	gcc -O3 -o ms ms.c streec.c rand1.c -lm

The compiler prints out a few warnings, but you can
ignore them.

Test it out with:

	./ms 5 2 -t 6.0 

This results in five simulated haplotypes in two data sets. 
Each column is a segregating site with two alleles, 0 and 1. 
See the program documentation for the meaning of the 
parameter 6.0.

Compiling COSI:
---------------

Again, let's assume you have cosi_1.1.tar on your desktop.
Then type in the terminal:

	cd ~/Desktop
	tar xf cosi_1.1.tar
	cd cosi_package
	make all

How to run COSI (if you are currently in the directory 
cosi_package) with the parameters fitted to generate
realistic-looking data:
	
	cd examples/bestfit
	perl run.pl
	
See files out.hap-? and out.pos-? for simulation output
for different simulated populations; replace the '?' with
the desired population index (see the 'params' file).
Files params and recParams contain simulation parameters,
such as the number of haplotypes you wish to generate for
each population.
The documentation for COSI is rather sparse, but some can
be found in the file cosi_package/documentation/guide.1.0