We found that, for both simulated and empirical data, our new model outperformed other methods in many situations. 
THERM
Performing Parentage Analysis in the Presence of Inbreeding and Null Alleles.Parentage analysis is an important method that is used widely in zoological and ecological studies.  Current mathematical models of parentage analyses usually assume that a population has a uniform genetic structure and that mating is panmictic.  The true father of a given offspring may thus be erroneously excluded in parentage analyses, or may have a low or negative LOD score.  Here, we present a new mathematical model to estimate parentage that includes simultaneously the effects of inbreeding, null alleles, and negative amplification.  We make available our methods in a new, free software package entitled parentage This can be downloaded via http://github.com/huangkang1987/parentage.
parentage