Revision 1 of PAP resulted from experience at the University of Utah in implementing versions of the pedigree analysis programs written by Elizabeth Thompson [1976, 1977]. A separate version evolved for each problem encountered (linkage, cancer penetrance functions, calculation of genotypic probabilities). PAP represented an attempt to include many applications in one program as well as to minimize user errors. Revision 1 derived directly from programs for zero- loop and arbitrarily complex pedigrees by Thompson [1976, 1977] and a zero- loop version for linkage by Kravitz [1979]. The terminology followed Cannings et al [1978] and PAP computed joint likelihoods as in Cannings et al [1976b].
Many people participated in the development of Revision 1. Mark Skolnick originated the idea and promoted its implementation. Tim Bishop originally incorporated GEMINI into the likelihood calculation structure and wrote the initial genotypic probability subroutine. Jean- Marc Lalouel assisted with the development of the original polygenic model and major locus/polygenic mixed models which used polychotomies. Kerry Kravitz, Chris Cannings, Elizabeth Thompson, Jon Hill, Dorit Carmelli and others contributed to discussions on scaling, efficient memory utilization and other problems.
Revision 2 of PAP resulted from the need to make the source code more portable to facilitate its installation by other users. Peter Cartwright assisted in modifying the source code.
Revision 3 of PAP responded to my own and other users' desires for a larger repertoire of genetic models. Feedback from many PAP users (Pat Moll, Patti Kramer, Candace Kammerer, and Jean MacCluer among others) provided invaluable suggestions which made Revision 3 more versatile and easier to use. In particular, Pat Moll continually contributed advice and encouragement; she also computed likelihoods of the variance components models using her program for testing the corresponding models in PAP. Peter Cartwright again assisted with technical aspects of the distribution of PAP.
Revision 4 of PAP incorporates the changes and additions that have accumulated over the intervening four and a half years since Revision 3 was released. Andy Marks assisted with technical aspects of the distribution of PAP.
Revisions 1 and 2 were supported by NIH grants T32 AM-07115, CA- 16573, GM- 27192 and HL- 21088. Revisions 3 and 4 were supported by NIH grant HD-17463.