Calculation of genotype probabilities

I am calculating genotype probabilities for PrP gene in our local sheep breeds. I am using iterative allelic peeling with incomplete penetrance (Thallman et al., 2001a, 2001b) as implemented in the GenoProb program, written by Thallman. Yes, I am using his method since he was kind enough to share the software with me. Of course, the methods does what I need. I did a bit of research on the available methods and from what I see one can use the following for animal livestock pedigrees:

• iterative peeling (see van Arendonk et al., 1989 and papers citing it!),
  
• Elston-Stewart iterative peeling (ESIP) sampler (Fernández et. al, 2001),
  
• descent graphs samplers (see Henshall and Tier, 2003) and
  
• allelic peeling (Thallman et al., 2001a, 2001b).

Get ready for some heavy reading if you dicided to look at the papers, especially the Fernández et. al (2001). Their method really seems great, but I got lost in the details. Huh, and I almoast always say that authors do not put enough details in the papers. It is probably just the problem that I have a hard time following their paper. There is a nice overview of methods for calculation of genotype probabilities at the beginning of their paper!

Fernández, S. A., Fernando, R. L., Guldbrandtsen, B., Totir, L. R. & Carriquiry, A. L. Sampling genotypes in large pedigrees with loops. Genetics Selection Evolution 33, 337-367 (2001). http://dx.doi.org/10.1051/gse:2001122

Henshall, J. M. and Tier, B. An algorithm for sampling descent graphs in large complex pedigrees efficiently. GR, 2003, 81(3):205-212. http://dx.doi.org/10.1017/S0016672303006232

Thallman, R. M. and Bennet, G. L. and Keele, J. W. and Kappes, S. M. Efficient computation of genotype probabilities for loci with many alleles: I. Allelic peeling. JAS, 2001a, 79(1):26-33. http://jas.fass.org/cgi/reprint/79/1/26

Thallman, R. M. and Bennet, G. L. and Keele, J. W. and Kappes, S. M. Efficient computation of genotype probabilities for loci with many alleles: II. Iterative method for large, complex pedigrees. JAS, 2001b, 79(1):34-44. http://jas.fass.org/cgi/reprint/79/1/34

van Arendonk, J. A. M. and Smith, C. and Kennedy, B. W. Method to estimate genotype probabilities at individual loci in farm livestock. TAG, 1989, 78:735-740.