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SIMULATION PROGRAMS

GASP (Genometric Analysis Simulation Program)
*Description Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models.
Authors A.F. Wilson, J.E.Bailey-Wilson, E.W. Pugh, A.J.M. Sorant (NCHGR/NIH)
References
  • Am Soc Hum Genet annual meeting 1996
  • Wilson AF, Bailey-Wilson JE, Pugh EW, Sorant AJM. (1996). The genometric analysis simulation program (G.A.S.P.): a software tool for testing and investigating methods in statistical genetics. Am J Hum Genet, Suppl. 59, A193
  • documentation draft (in postscript)
Website http://www.nhgri.nih.gov/DIR/IDRB/GASP/

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PopGene (Population Genetic)
Description PopGene performs the simulations commonly used in population genetics. The flexible, easy interface allows the viewing of parameters, graphics and results. PopGene provides simulations for basic as well as more complex models.
Authors Francis Yeh, Rong-Cai Yang and Timothy Boyle
Website http://www.ualberta.ca/~fyeh/popgene_info.html

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SIBSIM
*Description Simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. It is based on XML, completely written in C++ and published under the GNU General Public License.
Authors Daniel Franke (University Hospital Schleswig-Holstein)
Website http://dfranke.users.sourceforge.net/

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SIMLA (SIMulation of pedigree data for Linkage and Association studies)
*Description SIMLA is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.
Authors Elizabeth Hauser, Eden Martin, Meredyth Bass
References
  • Bass M, Martin E, Hauser E. (2002). Software for simulation studies of complex traits: SIMLA. Am J Hum Genet, 71, 569.
  • Bass M, Martin E, Hauser E. (2004). Proceedings of the Pacific Symposium on Biocomputing, in press.
Website http://www.chg.duke.edu/research/simla.html

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SIMLINK
*Description A computer program to estimate the probability ("power") of detecting linkage given family history information on a set of identified pedigrees.
Authors Michael Boehnke
References
  • Boehnke M. (1986). Estimating the power of a proposed linkage study: a practical computer simulation approach. Am J Hum Genet, 39, 513-527.
  • Ploughman LM, Boehnke M. (1989). Estimating the power of a proposed linkage study for a complex genetic trait. Am J Hum Genet, 44, 543-551.
  • online documentation (version 4.1, april 1990)
Website http://csg.sph.umich.edu/boehnke/simlink.php

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SIMULATE
*Description A program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package.
Authors Joe Terwilliger (Columbia University), Jurg Ott (Rockefeller University)
References

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* Description retrieved from http://linkage.rockefeller.edu/soft/