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A. Genocluster

Genocluster is a software to cluster automatically the two-dimensional data of individual SNP genotypes, for example the data produced by Invader Assay system.  The software should be excecuted in the Linux (UNIX) environment.

B. The procedure to install and excecution

1. Dissolve Genocluster.tar.gz

% tar xvzf Genocluster.tar.gz

2.  The directories "automation", "genocluster", and "simulation_figure" as well as the file "readme.txt" is made.

3. Go to the genocluster directory
 
cd genocluster
 
4. Type "make" to compile and link files.

make

C. How to excecute the software
There are two methods to excecute the software.  One is to excecute directly by the excecution file, and the other is to excecute it using "ruby".

1. Excecute directly

Excecute "genocluster" that had been made by "make".
 
% ./genocluster
 
-----select function-------
please select "4".
---------------------------
 
Inputfile2 name=./simulationdata/fig1/fig1.input2 # for example
Inputfile name=./simulationdata/fig1/fig1.input   # for example
(It may take a while to complete the computation)
Enter filename to record results.
result.txt # for example

2. Excecution using "ruby"
"ruby" should have been installed in the environment
a. Move to automation directory and excecute "ruby".
 
% cd ../automation
% ruby auto.rb
 
------function-----
please select "1"
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b. The following command will make figures in eps.
 
% ruby auto.rb
 
------function-----
please select "2"
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D. The two types of data files should be prepared as input files for the excecution.
One is the datafile and the other is NTC file including the information about the point of origin of the graph. Examples of the files are in the simulationdata directory.