UTILITY PROGRAMS
- GLUE (Genetic Linkage User Environment)
- GSMA (Genome Search Meta Analysis)
- KIN (KINship coefficients)
- MEGA2 (Manipulation Environment for Genetic Analyses)
- MINSAGE (MINimal SAmple size for GEnotypes)
- MKGST (Michael Krawczak's Genetics Software Tools)
- PAWE (Power for Association With Error)
- PBAT (Power calculation of family-Based Association Tests)
- QUANTO
- SILCLOD (SIgnificance Levels and Critical LODs)
- TDT-PC (Transmission Disequilibrium Test Power Calculator)
- TDTASP
- TDTPOWER
- TDTQ5 (Power Calculations for TDT)
| GLUE (Genetic Linkage User Environment) | |
| *Description | A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users. |
| Authors | Frank Dudbridge |
| References | Demo |
| Website | http://portal.litbio.org/Registered/Webapp/glue/ |
| 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 |
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| Website | http://www.kcl.ac.uk/depsta/memoge/gsma/ |
| 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. Tinker, Diane 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. |
| Website | ftp://gnome.agrenv.mcgill.ca/software/KIN/ |
| 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 |
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| Website | http://watson.hgen.pitt.edu/register/ |
| 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.uni-luebeck.de/pub/minsage/index.html |
| 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 |
| 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://linkage.rockefeller.edu/pawe/ |
| 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 |
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| Website | http://www.biostat.harvard.edu/~clange/default.htm |
| 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 |
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| Website | http://hydra.usc.edu/GxE |
| 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.uni-luebeck.de/pub/silcLOD/index.html |
| 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://www.biostat.jhsph.edu/~wmchen/pc.html |
| 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 | http://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.aspx?Software_Id=20 |
| 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. |
| Website | http://www.uni-bonn.de/~umt70e/soft.htm |
TDTQ5 (Power Calculations for TDT)  | |
| Description | This program estimates powers for specified sample sizes, or vice versa, for TDTQ5 method by Allison DB (1997). This program also estimates proportion of informative trios to the total number of trios needed to sample, for the specified parameters. |
| Authors | David B. Allison |
| References | Allison, D. B. (1997). Transmission Disequilibrium Tests for Quantitative traits. Am J Human Genetics, 60, 676-690. |
* Description retrieved from http://linkage.rockefeller.edu/soft/