PolyPatEx: an R package for paternity exclusion in autopolyploids

Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species and several software packages exist for elucidating paternity in diploids, however these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and a lack of available software. We introduce PolyPatEx, an R package for paternity exclusion analysis using microsatellite data in autopolyploid, monoecious or dioecious/bisexual species with a ploidy of 4n, 6n or 8n. Given marker data for a set of offspring, their mothers, and a set of candidate fathers, PolyPatEx uses allele matching to exclude candidates whose marker alleles are incompatible with the alleles in each offspring-mother pair. PolyPatEx can analyse marker data sets in which allele copy numbers are known (genotype data) or unknown (allelic phenotype data) – for data sets in which all...