SEGREGATION PROGRAMS

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)
Website	http://hasstedt.genetics.utah.edu/

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
Website	http://darwin.cwru.edu/sage/

SEGPATH
Description	Based on path analysis model.
Authors	Michael A. Province
References	Province MA, Rao DC. (1995). General purpose model and a computer program for combined segregation and path analysis (SEGPATH): Automatically creating computer programs from symbolic language model specifications. Genetic Epidmiology, 12, 203-219. Province MA, Rice TK, Borecki IB, Gu C, and Rao DC. (2001). A multivariate and multilocus variance components method based upon structural relationships to assess quantitative trait linkage via SEGPATH. Genetic Epidemiology, 24(2), 128-138.
Website	http://www.biostat.wustl.edu/~mike/segpath/