Article Paternity validation and estimation of genotyping error rate...
This article provided deep information on the theory behind the pedigree analysis and parentage testing so that it can be simply possible to run parentage testing by some handy commands for calculating mendelian inconsistency and opposing homozygosity (OH matrix) in R and moreover R software works either in Win and linux.
Additionally the " hsphase" R package can calculate the OP matrix and has some useful plotting functions, other useful R packages are kinship2, pedigreemm, pedigree and GeneticsPed.