BLOCKS-V0.2: A BRIEF DESCRIPTION OF THE SOFTWARE PACKAGE

Oct 10, 2002 
MK

Contents 
o Description
o Updates
o People
o References


DESCRIPTION

Blocks-v0.2 is a software package for analysis haplotype
data. It can be used for finding haplotype blocks, and for
measuring the strength of block boundaries. (The method is
described in detail in [1].) 

The software should work in all common Unix/Linux systems. 
However, it tested only in a Linux system. 

All directories and files are compressed into the file
blocks01.tgz. To uncompress, run 

	tar xvzf blocks02.tgz


Since some figures illustrating the results of the analysis
are automatically produced by the freeware program Gnuplot,
it is recomended that you have Gnuplot installed on your
system. 

For more details, see the instruction file that locates in 
the main directory. 

If you have comments and questions, please contact
mikko.koivisto@cs.helsinki.fi


UPDATES

The new 02-version includes the following improvements:

+ Visualization also using physical coordinates. 

+ In the k-means algorithm the Euclidean distance replaced
by the direct (correct) probability distance.

+ No penalization for missing values. 

+ k-means algorithm more robust.


PEOPLE 

The software package is implemented by 
M. Koivisto, M. Lukk, H. Mannila, K. Sood


REFERENCES

[1]	M. Koivisto, M. Perola, T. Varilo, W. Hennah, J. Ekelund,
	M. Lukk, L. Peltonen, E. Ukkonen, H. Mannila: An MDL method
	for finding haplotype blocks and for estimating the
	strength of haplotype block boundaries, 2002. (to appear
	in PSB'03)