In article <D1L64t.16t at news.cis.umn.edu>,
Dean Flanders <dean at scrapie.med.umn.edu> wrote:
>>Is there any software/protocols/papers/books that will help me in collapsing
>alleles? I have never done it, and would like to learn how to.
You may be interested in the following reference:
Braverman, M.S., "An Algorithm to Improve the Computational Efficiency
of Genetic Linkage Analysis", COMPUTERS AND BIOMEDICAL RESEARCH,
18, 24-36 (1985).
This article was inspired by Ott's original work on collapsing alleles,
but extends his ideas in two important ways (while still allowing you
to obtain the same likelihood ratio - not just an approximation):
1) it allows for pedigrees of arbitrary structure.
2) it allows for missing/partially known marker phenotypes.
Hope you find this helpful,
braver at cs.berkeley.edu