The program prepares pedigree data for calculation of Elston-Stewarts' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays.
The program is free software and you may get this package from http or ftp.
The program finds an optimal way to peel a pedigree having no loops in structure. If pedigree in data file has a loop, program stops with error message.
Assigning initial settings, opening file 'input_pedigree_file' or stop with error message.
Rewriting data of first pedigree in file as an array of nuclear families.
Finding an optimal peeling way.
It is assumed that finish point of optimal peeling way should be a nuclear family, in which both parents are founders, i.e. their parents are unknown. In this case, the number of possible ways corresponds to the number of such nuclear families. The program calculates the weight of each way and selects the way with minimal weight. The weight will determine running time while calculating likelihood function. Total peeling weight is a sum of peeling weights of all nuclear families peeled within pedigree. For each nuclear family, its peeling weight depends on peeling direction, offspring number and number of genotypes possible for family members: Gf*Gm*(Goff1+Goff2+...+Goffk) when peeling to parent, GoffP*Gf*Gm*(Goff1+Goff2+...+Goff[k-1]+1) when peeling to offspring, where
Output peeling sequences in output_file.
Nadezhda Belonogova (email@example.com)