The Pedigree Analysis Package (PAP) comprises a set of FORTRAN 77 programs for computing likelihoods [Elston & Stewart 1971] or simulating phenotypes on pedigree members using genetic models. PAP performs one of eight options selected at runtime: (1) compute the likelihood of specified parameter values, (2) compute the probability of each genotype for pedigree members, (3) simulate phenotypes for output into files, (4) maximize the likelihood over specified parameters (with or without standard errors), (5) compute the standard errors of parameters for known estimates, (6) simulate phenotypes and estimate parameter values, (7) estimate expected lod scores, (8) compute a grid of likelihoods over one or two parameters. Likelihood maximization uses either GEMINI [Lalouel 1979], for which the source is provided, or NPSOL [Gill et al 1986], for which the source must be purchased.
PAP may be used for segregation analysis, variance components analysis, linkage analysis, measured genotype analysis, or genetic model fitting. The genetic model may contain any number of loci and alleles. Model flexibility follows from the user selecting frequency, transmission, discrete major locus, quantitative major locus, and within genotype subroutines from a library of each, thereby specifying the assumptions and parameterization for an analysis or simulation. Similar data flexibility in PAP allows the pedigrees to be any size or structure and contain multiple ancestral branches and inbreeding or exchange loops; traits may be discrete or quantitative. Phenotypes may be simulated assuming any model available in PAP.
Using PAP incurs as its only obligation the requirement to appropriately reference each use. In addition to this manual, published approximations or models should be referenced upon using the corresponding subroutine. Check the description of the selected subroutine in Appendix C for a reference.
This manual contains practical advice on performing likelihood analysis in addition to technical details of the usage of PAP. The chapters progress from basic to more complex information. Chapters II through V should be read by all users; Chapters VI and VII contain information of less general interest; the Appendix contains reference information not meant to be read sequentially.
Instructions for obtaining the PAP source code can be obtained by sending a e-mail message to info@howard.genetics.utah.edu designating the subject as "pap". Any questions or problems should be sent to info@howard.genetics.utah.edu designating the subject as "pap query" or "pap error". The source for NPSOL is available from Stanford Business Software, Inc., 2680 Bayshore Parkway, Suite 304, Mountain View, CA 94043 [(415) 962-8719, (415) 962-1869 (fax)]. The GEMINI manual can be obtained by sending a request which includes your postal address to the above e-mail address, to FAX: (801) 581-7796, or to Dr. Sandra Hasstedt, Department of Human Genetics, University of Utah, 2100 Eccles Institute of Human Genetics, Salt Lake City, UT 84112.