For this example I generated genotype data at 11 equally
spaced markers for 200 ASPs plus their parents using
ALLEGRO.  
The markers were at 0,10,...,90,100cM.  
Each marker had 4 equally-frequent alleles.  

For the first 100 families, there was a disease gene at 35cM.
The penetrances for this gene were (.05,.9,.9), 
with a disease allele frequency of 0.015.  

For the next 100 families, there was a disease gene at 65cM.  
The penetrances for this gene were also (.05,.9,.9), 
with a disease allele frequency of 0.015.

I then combined data for all 200 families in the file
peds.txt. 

I then:  
1) Ran Genehunter using ch.g as the input file, i.e.
   gh.sun <ch.g 
2) Replaced all the dashes (between pairs of sib ids) with spaces
3) Ran fileprep.sas in sas to generate the files:  numsibs and sharing.  
4) Ran GEE2loc.fit.r1 using the command:
  GEE2loc.fit.r1 <geein >geeout

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References
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Allegro:

Gudbjartsson DF, Jonasson K, Frigge M, Kong A (2000) Allegro, a new computer
program for multipoint linkage analysis.  Nature Genetics 25:  12-13.

Genehunter:

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.

GEE2loc:

Biernacka JM, Sun L, Bull S.B.  (2004) Simultaneous localization of two linked
disease susceptibility genes.  Genet Epidemiol.  Published Online Oct 12 2004.
In press.