UTILITY PROGRAMS

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GSMA (Genome Search Meta Analysis)
*Description The GSMA is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included.
Authors Cathryn Lewis, Douglas Levinson, Lesley Wise
References
  • Wise LH, Lanchbury JS, Lewis CM. (1999). Meta-analysis of genome searches. Ann Hum Genet, 63(Pt 3):263-72
     
  • Levinson DF, Levinson MD, Segurado R, Lewis CM. (2003). Genome scan meta-analysis of schizophrenia and bipolar disorder, part I: Methods and power analysis. Am J Hum Genet, 73(1):17-33.
     
Website http://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/
researchgroups/clewis/software/GSMA/index.aspx

 

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KIN (KINship coefficients)
*Description Calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent)
Authors Nick A. TinkerDiane Mather (grain crops breeding and genetic research, McGill Univ), Jeff Reeve, Ying Wang, Rannala (Univ Alberta, Canada)
References Tinker NA, Mather DE. (1993). KIN: Software for computing kinship coefficients. Journal of Heredity, 84:238.
  Deprecated

 

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MEGA2 (Manipulation Environment for Genetic Analyses)
*Description Mega2 uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts).
Authors Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E Weeks
References
  • Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (1999), "Mega2, a data-handling program for facilitating genetic linkage and association analyses" (abstract), Am J Hum Genet 65:A436
     
  • FAQ-O-MATIC
Website https://watson.hgen.pitt.edu/register/

 

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MINSAGE (MINimal SAmple size for GEnotypes)
*Description Calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence.
Authors Andreas Ziegler
References Gregorius HG. (1980). The probability of losing an allele when diploid genotypes are sampled. Biometrics, 36:643-652.
Website http://www.imbs-luebeck.de/imbs/de/node/39

 

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MKGST (Michael Krawczak's Genetics Software Tools)
*Description A software package that includes ASP (power calculator for gene mapping using a sibpair design), ASPSHARE (rapid calculation of the expected ibd sharing at the trait locus, based upon the model), EASYPAT (calculation of likelihood ratios for single locus data, comparing specific types of simple hypotheses regarding the familial relationships involved), MUTPROF/MUTCOMP (comparison of mutation profiles), FINDSIRE (identify mothers or sires by means of the comparison of a large number of potential parents, typed at single locus DNA markers, with given infants or parent-infant duos), PATERN (calculation of paternity probabilities from the multilocus DNA profiles of trios, comprising mother, child and putative father)
Authors Michael Krawczak
Website http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

 

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PAWE (Power for Association With Error)
*Description Power and sample size calculations for genetic case-control association studies allowing for errors
Authors Derek Gordon assisted by Michael Nothnagel
References Gordon D, Finch SJ, Nothnagel M, Ott J. (2002). Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Human Heredity, 54: 22-33.
Website http://lab.rockefeller.edu/ott/programs

 

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PBAT (Power calculation of family-Based Association Tests)
*Description PBAT is an interactive software package that provides tools for the design and the data analysis of family-based association studies.
Authors Christoph Lange
References
  • Lange C, DeMeo D, Silverman EK, Weiss ST, Laird NM. (2003). Using the noninformative families in family-based association tests: A powerful new testing strategy. American Journal of Human Genetics, 73(4):801-11.
     
  • Lange C, DeMeo D, Silverman EK, Weiss ST, Laird NM. (2004). PBAT: tools for family-based association studies. American Journal of Human Genetics, 74(2):367-9.
Website http://www.hsph.harvard.edu/clange/default.htm

 

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QUANTO
*Description Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.
Authors Jim Gauderman, John Morrison
References
  • WJ Gauderman (2002), "Sample size requirements for matched case-control studies of gene-environment interaction", Stat Med 21:35-50.
  • WJ Gauderman (2002), "Sample size requirements for association studies of gene-gene interaction", American Journal of Epidemiology, 155:478-484.
  • WJ Gauderman (2003), "Candidate gene association studies for a quantitative trait, using parent-offspring trios", Genetic Epidemiology, 25:327-338.
  • http://biostats.usc.edu/Quanto.html
Website http://biostats.usc.edu/software

 

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SILCLOD (SIgnificance Levels and Critical LODs)
*Description Calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified.
Authors Andreas Ziegler
References Lander E, Kruglyak L. (1995). Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics, 11: 241-247.
Website http://www.imbs-luebeck.de/imbs/de/node/34

 

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TDT-PC (Transmission Disequilibrium Test Power Calculator)
*Description TDT Power Calculator (TDT-PC) is a computer program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program.
Authors Wei-Min Chen, Hong-Wen Deng (John Hopkins)
References Chen W. Deng H. (2001). A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes. Genetic Epidemiology, 21: 53-67.
Website http://people.virginia.edu/~wc9c/TDTPC/Download.htm

 

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TDTASP
*Description Power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic.
Authors Barry W. Brown, Dan Serachitopol
References Draft of paper describing method:
ftp://odin.mdacc.tmc.edu/private/bwb/tdtasp.pdf
ftp://odin.mdacc.tmc.edu/private/bwb/tdtasp.ps
Website https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.aspx?Software_Id=20

 

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TDTPOWER
*Description Calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT.
Authors Michael Knapp (Univ Bonn)
References Knapp M. (1999). A note on power approximations for the transmission/disequilibrium test. American Journal of Human Genetics, 64: 1177-1185.
  Deprecated

 

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