Polyploid paternity exclusion by allele matching.
PolyPatEx provides functions to perform paternity exclusion analysis in autopolyploid species having ploidy 4, 6, or 8. The package requires codominant marker data from two or more loci in a monoecious or dioecious species. The marker data can be 'genotypic' (copy numbers known) or 'phenotypic' (copy numbers not known). PolyPatEx can also perform exclusion on diploid (ploidy 2) genotype data.
Routines are provided to compare each progeny with its mother, and then with the candidate fathers, to determine which candidates are indeed capable of being fathers, on the basis of the allele sets they display at each locus.
PolyPatEx addresses the question - at a given locus, can the candidate father provide a viable gamete given its allele set, and given the possible paternal gametes indicated by the progeny's and mother's allele sets?
Note that PolyPatEx does not implement a probabilistic solution to the exclusion problem, merely a simple comparative analysis based on available alleles and their multiplicities. Also note that PolyPatEx is not optimised for very large marker datasets such as SNP datasets, instead is suited to low density, high information markers such as SSRs.
Alexander Zwart (alec.zwart at csiro.au)