The program GEE2loc.fit.r1 fits both the 1-locus and the 2-locus model by the GEE method.
(Here 1-locus refers to the fact that it is assumed there is exactly one disease gene in the region being studied.  Similarly, under the 2-locus model there are two linked disease genes in this region.)
The GEE method for localizing one disease gene was described by Liang et al. (2001).
The GEE method for localizing two linked disease genes was described by Biernacka et al. (2005).


If you use the software for any publication please reference:
Biernacka JM, Sun L, Bull SB (2004) Simultaneous localization of two linked disease susceptibility genes. Genet Epidemiol. Published Online Oct 12 2004. In press.


Detailed instructions for running this program are provided in the file documentation.GEE2loc.
In that file I have described the files that you will need to create prior to running GEE2loc (the input files), as well as the output that will be generated.

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Additional References
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Liang K-Y, Chiu YF, Beaty TH (2001a) A robust identity-by-descent procedure
using affected sib-pairs: multipoint mapping for complex diseases. Human
Heredity 51: 64-78.

Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and
nonparametric linkage analysis: A unified multipoint approach. The American Journal of Human Genetics 58: 1347-1363.


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Contact Information
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If you have any questions regarding GEE2loc please contact:

Joanna Biernacka
email: biernac@fisher.utstat.utoronto.ca or biernac@mshri.on.ca
phone: 1-416-586-4800 x 7539