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PAP (Pedigree Analysis Package)
*Description It can perform (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 unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models.
Authors Sandra Hasstedt (Univ Utah), Peter Cartwright contributed to versions 2 and 3; many others contributed to version 1 (Univ Utah)
References manual (version 5, PDF) (from Wellcome Trust)


SAGE (Statistical Analysis for Genetic Epidemiology)  
*Description SEGREG module of SAGE performs the segregation analysis.
Authors R. Elston, J. Bailey-Wilson, G. Bonney, L. Tran, B. Keats, A. Wilson


* Description retrieved from