PedConvert reads pedigree, phentoype and map files and converts them to specific output file format under each chromosome subfolder. DownCode program is used for estimating allele frequencies from pedigree file for Analyze, Genehunter and Solar and re-coding alleles (starting from number 1) for Analyze and Genehunter is required, since those programs need "numbered" alleles. DownCode reads alleles as "strings", which makes impossible to have alleles as non-numbers in original pedigree files.
Example of DownCode output:
All files are stored in chromosomal subfolders and are left there after analysis. So manual re-analysis is possible if desired.