# PedPeel

### DESCRIPTION

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.

### Download

The program is free software and you may get this package from http or ftp.

### PROGRAM BLOCKS

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.

#### STEP 0

Assigning initial settings, opening file 'input_pedigree_file' or stop with error message.

#### STEP 1

Rewriting data of first pedigree in file as an array of nuclear families.

#### STEP 2

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

- Gf,Gm,Goff[1..k]-number of genotypes possible for father, mother and each offspring, relatively;
- k - offspring number of the nuclear family;
- GoffP - number of genotypes possible for an offspring pointer. Numbers of possible genotypes are assigned from genotyping status ('gen' column of input file).

#### STEP 3

Output peeling sequences in output_file.

### AUTHOR

Nadezhda Belonogova (adg101@mail.ru)