- GAIA
- full name: Genetic Association Interaction Analysis
- version: 1.1 (2006)
- descriptions: GAIA is an easy to use, web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis.
- authors: Stuart Macgregor (QIMR, Brisbane, Australia and Cardiff University, UK) (email: stuart.macgregor@qimr.edu.au), Imtiaz Khan
- web/ftp: http://www.bbu.cf.ac.uk/html/research/biostats.htm
- source code language: perl, R
- operating systems: web-based
- executables:
- reference: Macgregor and Khan (2006), "GAIA: An easy-to-use web-based application for interaction analysis of case-control data", BMC Medical Genetics, 7:34. [abstract]
- GAP
- full name: genetic analysis package
- version: 1.0
- descriptions: a comprehensive package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors.
- authors: "Epicenter Software": Jonathan Buckley (Dept of Preventive Medicine, USC, jbuckley@hsc.usc.edu), Jim Gauderman, Duncan Thomas, Cheryl Faucett and John Morrison ( jmorr@rcf.usc.edu).
- web/ftp: http://www.epicentersoftware.com/products.php
- source code language: c++
- operating systems: MS-Windows (3.1/95/NT), UNIX(Solaris)
- executables:
- reference:
- availability: price single user: US$795; LAN version: US$1295. Kindred only: US$495. (academic prices are US$595, US$1095, US$395, respectively)
- GAS
- full name: Genetic Analysis System
- version: 2.0 (Dec 1995)
- descriptions: statistical analysis of genetic linkage data, sib-pair analysis, association studies
- authors: Alan Young ( ayoung@vax.ox.ac.uk )
- web/ftp: http://users.ox.ac.uk/~ayoung/gas.html .
- source code language:
- operating systems: MS-DOS, UNIX(SunOS/Solaris/AIX/OSF1/Ultrix/SGI-IRIX),VMS
- executables:
- reference:
- GAS2
- full name: statistical significance in Genomewide Association Studies in 2-stage
- version:
- descriptions: Evaluating Statistical Significance in Two-Stage Genomewide Association Studies
- authors:
- web/ftp: http://www.bios.unc.edu/~lin/software/GAS2/
- source code language: FORTRAN77
- operating systems:
- executables:
- reference: Lin (2006), "Evaluating statistical significance in two-stage genomewide association studies", American Journal of Human Genetics, 78(3):505-509. [html]
- GASP
- full name: Genometric Analysis Simulation Program
- version: 3.31 (April 1998)
- descriptions: 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 ( afw@nhgri.nih.gov), J.E.Bailey-Wilson, E.W. Pugh, A.J.M. Sorant (NCHGR/NIH)
- web/ftp:
http://www.nhgri.nih.gov/DIR/IDRB/GASP/
ftp://nhgri.nih.gov/pub/outgoing/gasp - source code language: FORTRAN77
- operating systems: UNIX(DEC-UNIX 4.0B/Solaris 2.5/SGI-IRIX 6.2/..)
- executables:
- reference: Am Soc Hum Genet annual meeting 1996 (Wilson, Bailey-Wilson, Pugh, Sorant, Am J. Hum Genet, suppl, 59, A193 (1996) ); documentation draft (in postscript)
- GASSOC
- full name: Genetic ASSOCiation analysis software for cases and parent
- version: 1.06 (Jun 2001)
- descriptions: Statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms.
- authors: D.J. Schaid ( schaid@mayo.edu), C. M. Rowland (Mayo Clinic/Foundation)
- web/ftp: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
- source code language: C
- operating systems: UNIX(SunOS/Solaris/..)
- executables:
- reference:
Am Soc Hum Genet annual meeting 1996
(Rowland, Schaid, Am J. Hum Genet, suppl, 59, A234 (1996) ).
Schaid (1996), Genetic Epidemiology, 13:423-449.
- GC/GCF
- full name: Genomic Control
- version:
- descriptions: GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values.
- authors: B Devlin, K Roeder
- web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm
- source code language: R
- operating systems: Linux
- executables:
- reference:
Devlin, Roeder (1999),
"Genomic control for association studies", Biometrics, 55:997-1004.
Bacanu, Devlin, Roeder (2002), "Association studies for quantitative traits in structured populations", Genetic Epidemiology, 22:78-93.
Devlin, Bacanu, Roeder (2004), "Genomic control in the extreme", Nature Genetics, 36(11):1129-1130.
- GCHAP (see also GENEPI.JAR )
- full name: Gene Counting method for HAPlotype analysis
- version:
- descriptions: By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.
- authors: Alun Thomas (email: alun@genepi.med.utah.edu)
- web/ftp: http://episun7.med.utah.edu/~alun/gchap/index.html
- source code language: Java
- operating systems:
- executables:
- reference:
Thomas (2003),
"GCHap: fast MLEs for haplotype frequencies by gene counting",
Bioinformatics, 19:2002-2003.
Thomas (2003), "Accelerated gene counting for haplotype frequency estimation", Annals of Human Genetics, 67:608-612.
- GDA
- full name: Genetic Data Analysis
- version: 1.0d16c (Jan 2001)
- descriptions: designed to accompany the second edition of Bruce Weir's book "Genetic Data Analysis" (1996. Sinauer Associates)
- authors: Paul Lewis, Dmitri Zaykin
- web/ftp: http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
- source code language:
- operating systems: MS-Windows (3.1/95/NT), MacOS (10.2.8/10.3)
- executables:
- reference:
- GEMS
- full name: Genetic Epidemiology ModelS
- version: 1.0
- descriptions: a computer software for fitting Genetic Epidemiology Models. This version of GEMS provides the features for many statistical analyses of family data:
- authors: GE Bonney, V Apprey, J Kwagyan (Howard Univ)
- web/ftp: http://statgen.genomecenter.howard.edu/gems.htm
- source code language:
- operating systems: UNIX(DEC-alpha), Linux
- executables: gems
- reference: Am Soc Hum Genet annual meeting 1997 (Bonney, Slater, Slifker, Am. J. Hum. Genet. suppl 61, A212 (1997) ); Bonney, Apprey, Kwagyan (2001), "A computer software for fitting Genetic Epidemiology Models", tech report 2001-02.
- GENECLASS
- full name:
- version: v2.0g (Jan 2005)
- descriptions: GENECLASS2 is a program employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection).
- authors: Jean-Marie Cornuet
- web/ftp: http://www.montpellier.inra.fr/URLB/
- source code language: Delphi
- operating systems: MS-Windos, UNIX
- executables:
- reference: Piry, Alapetite, Cornuet, Paetkau, Baudouin, Estoup (2004), "GeneClass2: a software for genetic assignment and first-generation migrant detection", Journal of Heredity, 95:536-539.
- GENECOUNTING
- full name:
- version: 2.2
- descriptions: gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data
- authors: Jinghua Zhao (MRC Epidemiology Unit at Strangeways Research Lab, UK) (email: jinghua.zhao@mrc-epid.cam.ac.uk )
- web/ftp: http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/
- source code language: C
- operating systems: MS-Windows, UNIX(Solaris), Linux
- executables:
gc, gcp, gcx, pgc.
RUNGC, SCANASSOC, COMPGR, SCANGROUP, LDPAIRS - reference:
Zhao, Lissarrague, Essioux, Sham (2002),
"GENECOUNTING: haplotype analysis with missing genotypes",
Bioinformatics, 18(12):1694-1695.
Zhao (2004), "2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis", Bioinformatics, 20:1325-1326.
Curtis, Knight, Sham (2006), "Program report: GENECOUNTING support programsProgram report: GENECOUNTING support programs", Annals of Human Genetics, 70:277-279.
- GENEFINDER
- full name:
- version: 1.1.9 (June 2004)
- descriptions: GeneFinder uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.
- authors: Wei-Min Chen (email: wechen@jhsph.edu), Kung-Yee Liang (email: kyliang@jhpsh.edu), Yen-Feng Chiu
- web/ftp: http://www.biostat.jhsph.edu/~wmchen/gf.html
- source code language: C++
- operating systems: MS-Windows, MS-DOS, UNIX(Solaris)
- executables: gf
- reference:
Liang KY, Zeger SL (1986),
"Longitudinal data analysis using generalized
linear models",
Biometrika, 73: 13-22.
Liang KY, Chiu YF, Beaty TH (2001), "A robust identity by descent procedure using affected sib pairs: a multipoint approach for complex diseases", Human Heredity, 51:64-78.
Liang KY, Chiu YF, Beaty TH, Wjst Matthias (2001), "A multipoint analysis using affected sib pairs: incorporation of linkage evidence from unlinked regions", Genetic Epidemiology, 21:105-122.
Liang KY, Huang CY, Beaty TH (2000) A unified sampling approach for multipoint analysis of qualitative and quantitative traits in sib pairs. American Journal Human Genetics, 66(5):1631-1641. [abstract]
Glidden DV, Liang KY, Chiu YF, Pulver AE (2003), "Multipoint affected sibpair linkage methods for localizing susceptibility genes of complex diseases", Genetic Epidemiology, 24:107-117
- GENEHUNTER (see also ALLEGRO, GENEHUNTER-IMPRINTING, GENEHUNTER-MODSCORE, GENEHUNTER-PLUS, GENEHUNTER-TWOLOCUS )
- full name:
- version: 2.1 release 4 (April 2003)
- descriptions: multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction
- authors: Leonid Kruglyak ( leonid@genome.wi.mit.edu), Mark Daly (mjdaly@genome.wi.mit.edu), Mary Pat Reeve-Daly ( mpreeve@genome.wi.mit.edu), Eric Lander ( lander@genome.wi.mit.edu ) (Whitehead Institute)
- web/ftp: http://www.broad.mit.edu/ftp/distribution/software/genehunter/
- source code language: C
- operating systems: UNIX
- executables: gh
- reference:
Kruglyak,Daly,Reeve-Daly,Lander (1996),
"Parametric and nonparametric linkage analysis: a unified multipoint approach",
American Journal of Human Genetics, 58:1347-1363.
[abstract]
online documentation (2.0beta)
documentation (in PDF ) (2.0beta).
online instruction (1.1, from Falling Rain Genomics, Inc.)
Am J Hum Genet, suppl, 65 ( abstract) (1999)
- GENEHUNTER-IMPRINTING (see also ALLEGRO, GENEHUNTER, GENEHUNTER-MODSCORE, GENEHUNTER-PLUS, GENEHUNTER-TWOLOCUS )
- full name:
- version: version: 1.3 (May 2000), 2.1 beta (Oct 2001).
- descriptions: GENEHUNTER-IMPRINTING is a modification of the GENEHUNTER software package (version 1.3). It allows to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect.
- authors: K Strauch strauch@med.uni-marburg.de) (Philipps University Marburg, Germany)
- web/ftp: http://www.staff.uni-marburg.de/~strauchk/software.html
- source code language: C
- operating systems: UNIX(SUNOS,Solaris,OSF,HPUX,AIX,Ultrix), Linux, MS-Windows
- executables: ghi, xghi
- reference: Strauch, Fimmers, Kurz, Deichmann, Wienker, Baur (2000), American Journal of Human Genetics, 66(6):1945-1957. [abstract]
- GENEHUNTER-MODSCORE
- full name:
- version: 2.0 (October 2006)
- descriptions: GENEHUNTER-MODSCORE is a further extension of GENEHUNTER-IMPRINTING. The program is based on the original GENEHUNTER version 2.1 release 6. GENEHUNTER-MODSCORE allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. As of version 2.0, it is possible to use sex-specific recombination frequencies. The genetic positions of markers can be automatically read from a publicly available genetic map.
- authors: Konstantin Strauch (strauch@med.uni-marburg.de) (Philipps University Marburg, Germany) Johannes Dietter (dietter@med.uni-marburg.de) (Philipps University Marburg, Germany)
- web/ftp: http://www.staff.uni-marburg.de/~strauchk/software.html
- source code language: C
- operating systems: UNIX(SUNOS,Solaris,OSF,HPUX,AIX,Ultrix), Linux, MS-Windows
- executables: ghm
- reference:
K Strauch (2003), "Parametric linkage analysis with automatic optimization
of the disease model parameters".
American Journal of Human Genetics 73(Suppl1):A2624.
Dietter, Mattheisen, Fuerst, Rueschendorf, Wienker, Strauch (2007), "Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE", Bioinformatics, 23(1):64-70.
- GENEHUNTER-PLUS (see also ALLEGRO, GENEHUNTER, GENEHUNTER-IMPRINTING, GENEHUNTER-MODSCORE, GENEHUNTER-TWOLOCUS )
- full name:
- version: 1.2 (Nov 1998)
- descriptions: GENEHUNTER-PLUS is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997).
- authors: Augustine Kong (kong@galton.uchicago.edu), Mike Frigge.
- web/ftp: http://galton.uchicago.edu/genehunterplus
- source code language: C
- operating systems:
- executables: ghp, xghp,asm
- reference: Kong, Cox (1997), "Allele-sharing models: LOD scores and accurate linkage tests", American Journal of Human Genetics, 61(5):1179-1188. [abstract]
- GENEHUNTER++SAD
- full name:
- version:
- descriptions: implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing
- authors: Mathieu Lemire (email: mlemire@sdf.lonestar.org)
- web/ftp: http://mlemire.freeshell.org/software.html
- source code language:
- operating systems:
- executables:
- reference: Lemire, Roslin, Laprise, Hudson, Morgan (2004), "Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3", American Journal of Human Genetics, 75:571-586.
- GENEHUNTER-TWOLOCUS (see also ALLEGRO, GENEHUNTER, GENEHUNTER-IMPRINTING, GENEHUNTER-MODSCORE, GENEHUNTER-PLUS )
- full name:
- version: 1.3 (May 2000), optimized and parallelized version (May 2004)
- descriptions: GENEHUNTER-TWOLOCUS is a modification of the GENEHUNTER software package (version 1.3). The program performs complete parametric and nonparametric multi-marker linkage analysis with two autosomal, biallelic disease loci.
- authors: K Strauch strauch@med.uni-marburg.de) (Philipps University Marburg, Germany), Johannes Dietter ( dietter@med.uni-marburg.de) (Philipps University Marburg, Germany)
- web/ftp: http://www.staff.uni-marburg.de/~strauchk/software.html
- source code language: C
- operating systems: UNIX(SUNOS,Solaris,OSF,HPUX,AIX,Ultrix), Linux, MS-Windows
- executables: ght
- reference:
Strauch, Fimmers, Kurz, Deichmann, Wienker, Baur (2000),
"Parametric and nonparametric multipoint linkage analysis with imprinting and two-locus-trait
models: application to mite sensitization",
American Journal of Human Genetics, 66(6):1945-1957.
[abstract]
Dietter, Spiegel, an Mey, Pflug, Al-Kateb, Hoffmann, Wienker, Strauch (2004): "Efficient two-trait-locus linkage analysis through program optimization and parallelization: application to hypercholesterolemia", European Journal of Human Genetics, 12:542-550.
- GENEPI.JAR
- full name:
- version: September 2006
- descriptions: a set of Java programs for genetic epidemiology analysis
- authors: Alun Thomas (University of Utah)
- web/ftp: http://bioinformatics.med.utah.edu/~alun/software/index.html
- source code language: Java
- operating systems: web-based
- executables: CheckFormat, CheckError, DownCodeAlleles, GeneCountAlleles, SelectLoci, SelectKindreds, TrimPed, TwoPointLods, MaxTwoPointLods, McLink, McLinkLD, HapGraph, GaploFreqs, GCHap, ApproxGCHap, ViewGraph, ViewPed, ViewLinkPed,
- reference:
- GENEPOOL
- full name:
- version: 0.84
- descriptions: GenePool is a software package that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. GenePool supports genotyping platforms from Affymetrix and Illumina.
- authors: John Pearson (Translational Genomics Research Institute) (email: jpearson@tgen.org) David Craig (email: dcraig@tgen.org) Matt Huentelman (email: mhuentelman@tgen.org) Waibhav Tembe, Sotiris Mitranopolous, Nils Homer
- web/ftp: http://genepool.tgen.org/
- source code language: C/C++/Perl
- operating systems: Linux, MacOS (should compile on most UNIX systems with gcc)
- executables: gpcommand, gpextract, gpanalyze
- reference: Pearson, Huentelman, Halperin, Tembe, Melquist, Homer, Brun, Szelinger, Coon, Zismann, Webster, Beach, Sando, Aasly, Heun, Jessen, Kolsch, Tsolaki, Daniilidou, Reiman, Papassotiropoulos, Hutton, Stephan, Craig (2007), "Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies", American Journal of Human Genetics, 80:126-139. [html]
- GENEPOP
- full name:
- version: 3.4
- descriptions: a population genetics software package
- authors: Michel Raymond (email: raymond@isem.univ-montp2.fr), Francois Rousset ( email: rousset@isem.univ-montp2.fr), Eleanor Morgan (email: nell@wbiomed.curtin.edu.au) (web version)
- web/ftp: http://wbiomed.curtin.edu.au/genepop/
- source code language:
- operating systems:
- executables:
- reference: Raymond, Rousset (1995), "GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism", Journal of Heredity, 86:248-249
- GENERECON
- full name:
- version:
- descriptions: GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
- authors: Thomas Mailund (email: mailund@birc.au.dk) (Univ of Oxford, UK and Univ of Aarhus, Denmark)
- web/ftp: http://www.daimi.au.dk/~mailund/GeneRecon/
- source code language: C++
- operating systems: UNIX, Linux, MacOS, MS-Windows
- executables:
- reference: Mailund, Schierup, Pedersen, Madsen, Hein, Schauser (2006), "GeneRecon -- A coalescent based tool for fine-scale association mapping", Bioinformatics, 22(18):2317-2318.
- GENESPRING GT (previously VARIA )
- full name:
- version: 2.0
- descriptions: GeneSpring GT is a desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated SNPs and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers.
- authors: Agilent Technologies (previously Silicon Genetics)
- web/ftp: http://www.chem.agilent.com/scripts/pds.asp?lpage=34662
- source code language:
- operating systems:
- executables:
- reference:
- price: for quote request, go to http://www.chem.agilent.com/scripts/cag_requestaquote.asp
- GENETIC POWER CALCULATOR
- full name:
- version: 2001-2005
- descriptions: automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests
- authors: S. Purcell, P Sham
- web/ftp: http://pngu.mgh.harvard.edu/~purcell/gpc/
- source code language:
- operating systems:
- executables:
- reference:
Sham, Cherny, Purcell, Hewitt (2000),
"Power of linkage versus association analysis of quantitative
traits, by use of variance-components models, for sibship data",
American Journal of Human Genetics, 66(5):1616-1630.
[abstract]
Purcell, Cherny, Sham (2003), "Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits", Bioinformatics, 19(1):149-150.
- GENETSIM
- full name:
- version:
- descriptions: GENETSIM provides flexible simulations of family data within an easy-to-use, high-level programming language. GENETSIM has no limit on pedigree sizes or structures, or number of families, or number of marker, or number of chromosomes. Genetic transmission is modeled by first generating the locations of recombination events, and then performing gene dropping according to the given recombination pattern. Any pattern of missing data can be specified and genotyping errors can be simulated. GENETSIM can simulat multiple QTLs with pleiotropic effects, multivariate polygenic background and any number of environmental factors, age effects, epistasis and variable expression. Users can also select families based on ascertainment schemes by repeating simulations.
- authors: Mike Miller, Na Li (Univ of Minnesota)
- web/ftp: http://taxa.epi.umn.edu/GenetSim/
- source code language: Octave, R (future version)
- operating systems:
- executables:
- reference: Miller, Li (2005), "GenetSim: software for simulation of familial data in genetics and epidemiology" (abstract), Genetic Epidemiology, 29:269.
- GENEWEAVER
- full name:
- version: 1.1 (2003)
- descriptions: software for charting family medical/health history
- authors:
- web/ftp: http://www.geneweaveronline.com/
- source code language:
- operating systems: MS-Windows (95/98/2000/NT/XP)
- executables:
- reference:
- availability: commercialUS$39.95
- GENIE
- full name:
- version: 2.6.2
- descriptions: GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests.
- authors: Nicola Camp, K Allen-Brady, Jathine Wong, K Curtin, R Abo
- web/ftp: http://bioinformatics.med.utah.edu/Genie/index.html
- source code language: Java 1.6
- operating systems: web-based
- executables:
- reference:
Allen-Brady, Wong, Camp (2006), "PedGenie: an analysis
approach for genetic association testing in extended pedigrees
and genealogies of arbitrary size",
BMC Bioinformatics, 7:209.
Curtin, Wong, Allen-Brady, Camp (2007), "PedGenie: meta genetic association testing in mixed family and case-control designs", BMC Bioinformatics, 8:448.
- GENOCHECK
- full name: GenoCheck
- version: 1.0 (sept 20, 1995)
- descriptions: GenoCheck is a program designed to identify genotypes that are likely to be errors. The statistical method was designed to identify typing error rather than pedigree errors, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance.
- authors: Meg Gelder Ehm (Glaxo Wellcome Inc. mge37216@glaxowellcome.com), Robert W. Cottingham, Marek Kimmel, Alejandro Schaffer, Ramana Idury, Shriram Krishnamurthi, Sandeep Gupta, G. Mark Lathrop
- web/ftp: http://softlib.rice.edu/geno.html
- source code language: C
- operating systems: UNIX
- executables: GenoCheck, toaff
- reference:
Ehm, Cottingham, Kimmel (1995), J. Biological Systems, 3(1), 13-25.
Ehm, Cottingham, Kimmel (1996), "Error detection for genetic data, using likelihood methods", American Journal of Human Genetics, 58(1):225-234. [abstract]
- GENOGRAM-MAKER
- full name:
- version:
- descriptions: a graphic way of organizing the mass of information gathered during a family assessment and finding patterns in the family system
- authors:
- web/ftp: http://www.genogram.org/
- source code language:
- operating systems: MS-Windows, MacOS
- executables:
- reference: Monica McGoldrick, Randy Gerson, , Sylvia Shellenberger (1999), Genograms: Assessment and Intervention , 2nd edition (W.W.Norton & Company).
- price: US$50 (student), US$125 (standard)
- GENOME
- full name:
- version:
- descriptions: GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model. The purpose of this program is to simulate sequences on the whole genome scale within practical time.
- authors: Liming Liang (email: lianglim@umich.edu), Sebastian Zollner, Goncalo Abecasis (University of Michigan)
- web/ftp: http://www.sph.umich.edu/csg/liang/genome/
- source code language: C++
- operating systems: UNIX(Solaris), Linux, MS-Windows
- executables:
- reference: Liang, Zollner, Abecasis (2006), "GENOME: a rapid coalescent-based whole genome simulator", ASHG Annual Meeting.
- GENOMESIMLA
- full name:
- version: beta
- descriptions: genomeSIMLA is a forward-time population simulation method that can simulate realistic patterns of LD in both family-based and case-control datasets.
- authors: Marylyn Ritchie (email: genomesimla@chgr.mc.vanderbilt.edu)
- web/ftp: http://chgr.mc.vanderbilt.edu/genomeSIMLA/
- source code language:
- operating systems:
- executables:
- reference: Dudek, Motsinger, Velez, Williams, Ritchie (2006), "Data simulation software for whole-genome association and other studies in human genetics", Pacific Symposium on Biocomputing, 499-510.
- GENOMIZER
- full name:
- version: 1.0
- descriptions: Genomizer is a platform independent Java program for the analysis of genome wide association experiments.
- authors: Andre Franke (email: a.franke@mucosa.de), Jochen Hampe
- web/ftp: http://www.ikmb.uni-kiel.de/genomizer/
- source code language: Java
- operating systems: MS-Windows, Linux
- executables:
- reference: Franke, Wollstein, Teuber, Wittig, Lu, Hoffmann, Nurnberg, Krawczak, Schreiber, Hampe (2006), "GENOMIZER: an integrated analysis system for genome-wide association data", Human Mutation, 27(6):583-588
- GENOOM
- full name: GENetic Object Oriented Modeling in population genetics
- version: 3.66 (November 2003)
- descriptions: GENOOM implements a virtual computer world where biological entities are digital objects. In this world, each individual of a population is represented by a set of chromosomes with genetic elements (markers, genes, Quantitative Traits Loci, etc.) and attributes (phenotype, age, fertility, living status, exposure, etc.). It comes with a built-in model allowing basic genetic studies by simulations, performed according to parameter values such a penetrance matrix (phenotype probabilities for each genotype), exposure, between-relative mating probabilities, and a probability of migration in a two-dimensional migration process. The simulated populations could be analysed with different packages for statistical or genetical analysis (e.g., SAS, S-PLUS, Linkage, Mapmaker/sibs, Genehunter). Pedigrees can also be simulated according to a pedigree file at the LINKAGE format.
- authors: Hadi Quesneville, Dominique Anxolabehere
- web/ftp:
http://dynagen.ijm.jussieu.fr/research/topics/modeling-complex-genetic-systems/object-oriented-modeling-of-complex-genetic-systems
ftp://ftp.ijm.jussieu.fr/Usr/quesneville/genoom/ - source code language: C++
- operating systems: UNIX, Linux
- executables:
- reference: Quesneville, Anxolabehere (1997), "GENOOM: a simulation package for GENetic Object-Oriented Modeling", Abstract in the European Mathematical Genetics Meeting Proceedings, Annals of Human Genetics, 61:543.
- GENOPROOF
- full name:
- version: 1.1 (July 2006)
- descriptions: download software package for the analysis of multiplex PCR kits within the scope of paternity testing, kinship cases and population studies. GenoProof® offers: (1) probably the most extensive existing population database for all supported markers of more than 50 ethnic groups, (2) individually configurable quality assurance options, (3) complex concept of user rights in order to guarantee data security, (4) languages German and English
- authors: Dr. F. Gotz (Qualitype AG, Dresden, Germany) (email: info@genoproof.de)
- web/ftp: http://www.genoproof.com or http://qualitype.de/genoproof/
- source code language: Java
- operating systems: MS-Windows (95/98/2000/NT/XP)
- executables:
- reference:
- GENTOOLS
- full name:
- version:
- descriptions: software for analysis and manipulation of genetic linkage data of genetic linkage data, including conversions of pedigree files between CRI-MAP and LINKAGE format.
- authors: Raymond Weaver, Cynthia Helms, Santosh Mishra, Helen Donis-Keller (Washington University School of Medicine, St. Lious)
- web/ftp:
http://www.genlink.wustl.edu/software/index.html
ftp://mapper.wustl.edu/pub/gentools - source code language: C
- operating systems: UNIX
- executables: faminfo, genlink, jim, pic, pichet, twotable,unmerge, inherit,linkgen,refbld,unmerge2
- reference: Weaver, Helms, Mishra, Donis-Keller (1992), "Software for analysis and manipulation of genetic linkage data", American Journal of Human Genetics, 50:1267-1274. [abstract]
- GERMLINE
- full name:
- version: 1.2.1 (September 2008)
- descriptions: GERMLINE is a program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.
- authors: Sasha Gusev (email: gusev@cs.columbia.edu)
- web/ftp: http://www1.cs.columbia.edu/~gusev/germline/
- source code language: C++
- operating systems: Linux
- executables:
- reference:
- GEST
- full name: Gene-Environment interaction and STability
- version:
- descriptions:
- authors: Yasuo Ukai (University of Tokyo, Japan)
- web/ftp: http://lbm.ab.a.u-tokyo.ac.jp/~ukai/gest98.html
- source code language:
- operating systems:
- executables:
- reference: Ukai, Nesumi, Yakano (1996), "A package of computer programs for the statistical analysis of genotype x environment interaction and stability GEST" (in Japanese), Breeding Science, 46:73-79.
- GEVALT
- full name: GEnotype Visualization and ALgorithmic Tool
- version: 2.0
- descriptions: GEVALT is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families.
- authors: Ofir Davidovich, Gad Kimmel, Eran Halperin, Oded Apel, Ron Shamir.
- web/ftp: http://acgt.cs.tau.ac.il/gevalt/
- source code language:
- operating systems:
- executables:
- reference: Davidovich, Kimmel, Shamir (2007), "GEVALT: An integrated software tool for genotype analysis", BMC Bioinformatics, 8:36.
- GGT (see also, MAPCOMP )
- full name: Graphical GenoTyping package
- version: December 2006
- descriptions: GGT combines genetic map data and locus data to display Graphical Genotypes. Data can be viewed by individual or by linkage group, and sorted on markers. Statistics are calculated and simultaneous filtering/selection on multiple linkage groups is possible. Output of hi-res genotype drawings directly to printer or to emf/jpeg/bitmap image. A module for constructing GGT-datafiles from common mapmaker/joinmap style formatted data is available.
- authors: Ralph van Berloo (Wageningen University, The Netherlands, ralph.vanberloo@wur.nl )
- web/ftp: http://www.dpw.wau.nl/pv/PUB/ggt/
- source code language: Delphi (Pascal)
- operating systems: MS-Windows (95/98/2000/XP)
- executables: GGT32.EXE
- reference: R Van Berloo (1999),"GGT: Software for the display of graphical genotypes", Journal of Heredity, 90:328-329. [ full text (PDF) : http://www.dpw.wau.nl/pv/papers/reprint/9903.pdf]
- GHOST
- full name:
- version:
- descriptions: GHOST is a software package for family-based genomewide association (GWA) analysis, with the ability to infer missing genotypes using the Elston-Stewart algorithm. When SNPs from an association panel are less complete (i.e., having more missing genotypes) than markers from a linkage panel, many of the missing genotypes can be determined. GHOST can handle large pedigrees -- when pedigrees are small, Merlin is also recommended for this analysis.
- authors:
- web/ftp: http://www.sph.umich.edu/csg/chen/ghost/
- source code language:
- operating systems:
- executables:
- reference:
Burdick, Chen, Abecasis, Cheung (2006),
"In silico method for inferring genotypes in pedigrees",
Nature Genetics, 38:1002-1004.
Chen, Abecasis (2007), "Family-based association tests for genomewide association scans", American Journal of Human Genetics, 81(5):913-926. [html]
- GIST
- full name: Genotype Ibd Sharing Test
- version: 0.3
- descriptions: testing whether the presence of a marker allale can partially account for the evidence of linkage in the region of the marker
- authors: Chun Li (Vanderbilt University). (email: chun.li@vanderbilt.edu)
- web/ftp: http://phg.mc.vanderbilt.edu/content/gist
- source code language:
- operating systems: UNIX, MS-Windows
- executables:
- reference: Li, Scott, Boehnke (2004), American Journal of Human Genetics, 74(3):418-431. [html]
- GLM
- full name: General Linkage Mapping database
- version:
- descriptions:
- authors: Paul Lucek ( prl1@columbia.edu ), Jurg Ott (Columbia Univ)
- web/ftp: ftp://linkage.rockefeller.edu/software/glm
- source code language: Paradox for DOS, Pascal
- operating systems: MS-DOS.
- executables:
- reference: Am Soc Hum Genet annual meeting 1994 (Lucek, Ott, Am J. Hum Genet, suppl, 55(3), A156 (1994) )
- GLUE
- full name: Genetic Linkage User Environment
- version: 3.30 (Aug 2002)
- descriptions: A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, 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 (email: frank.dudbridge@mrc-bsu.cam.ac.uk)
- web/ftp: http://portal.litbio.org/Registered/Webapp/glue/
- source code language: Perl
- operating systems: any web browser
- executables:
- reference:
- GMA
- full name: Genetic Mixture Analysis
- version:
- descriptions:
- authors: Steven T Kalinowski (email: skalinowski@montana.edu)
- web/ftp: http://www.montana.edu/kalinowski/GMA/GMA_Home.htm
- source code language:
- operating systems: MS-Windows
- executables:
- reference:
- GMCHECK
- full name:
- version:
- descriptions: GMCheck finds the posterior probabilities for data errors for genotypes and phenotypes in pedigree data
- authors: Alun Thomas (email: alun@genepi.med.utah.edu)
- web/ftp: http://episun7.med.utah.edu/~alun/gmcheck/
- source code language: Java
- operating systems:
- executables:
- reference: Thomas (2005), "GMCheck: Bayesian error checking for pedigree genotypes and phenotypes", Bioinformatics, 21(14):3187-3189.
- G-MENDEL
- full name:
- version: 3.0 (May 1994)
- descriptions: a tool for construction of genetic linkage maps and analyzing Mendelian phenotypes.
- authors: J.L Holloway, S.J. Knapp (Department of Crop and Soil Science, Oregon State University)
- web/ftp: http://cropandsoil.oregonstate.edu/G-mendel
- source code language:
- operating systems: UNIX, MS-Windows
- executables:
- reference:
- GOLD
- full name: Graphical Overview of Linkage Disequilibrium
- version: November 2001
- descriptions: A software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.
- authors: G R Abecasis, William Cookson (Wellcome Trust Centre for Human Genetics, Oxford, UK)
- web/ftp: http://www.sph.umich.edu/csg/abecasis/GOLD/
- source code language:
- operating systems:
- executables:
- reference: Abecasis, Cookson (2000), Bioinformatics, 16(2):182-183.
- GREGOR
- full name:
- version:
- descriptions: the program allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection.
- authors: Nick Tinker ( tinker@agr.gc.ca ), Diane Mather (grain crops breeding and genetic research, McGill Univ, mather@agradm.lan.mcgill.ca)
- web/ftp:
http://gnome.agrenv.mcgill.ca/tinker/gregor.htm
ftp://gnome.agrenv.mcgill.ca/software/GREGOR/ - source code language:
- operating systems: MS-DOS
- executables:
- reference: Tinker and Mather, Journal of Heredity, 84, 237 (1993)
- GRIDQTL
- full name:
- version: 1.5.1 (August 2010)
- descriptions: A publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models.
- authors:
- web/ftp: http://www.gridqtl.org.uk/
- source code language:
- operating systems: web-based
- executables:
- reference:
- GRONLOD
- full name: GRONingen university LOR score calculation
- version:
- descriptions: Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood.
- authors: Gerard te Meerman (University of Groningen, The Netherlands) (g.j.te.meerman@med.rug.nl)
- web/ftp:
- source code language: PROLOG
- operating systems: MS-Windows (3.1/95/NT)
- executables: gronrec,gronreca,gronlod,groninbr, gronchec,gronped,gronpedc, grontree
- reference: Meerman, "A Logic Programming Approach to Pedigree Analysis", (Thesis Publishers Amsterdam, 1991). Available free of charge from the author. Contains documented sources and description.
- GRR
- full name: Graphical Representation of Relationships
- version: Aug 2003
- descriptions: a graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data.
- authors: G R Abecasis (email: goncalo@well.ox.ac.uk ), S S Cherny (email: cherny@qtl.well.ox.ac.uk ), W O C Cookson, and L R Cardon (email: lon@well.ox.ac.uk )
- web/ftp: http://www.sph.umich.edu/csg/abecasis/GRR/
- source code language: C++
- operating systems: MS-Windows
- executables:
- reference: Abecasis, Cherny, Cookson, and Cardon (2001), "GRR: Graphical representation of relationship errors", Bioinformatics, 17(8):742-743.
- GS-EM
- full name: GenoSpectrum Expectation-Maximuzation
- version:
- descriptions:
- authors:
- web/ftp: http://www.people.fas.harvard.edu/~junliu/genotype/
- source code language:
- operating systems:
- executables:
- reference: Kang, Qin, Niu, Liu (2004), "Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms", American Journal of Human Genetics, 74(3):495-510. [html]
- GSMA
- full name: Genome Search Meta Analysis
- version:
- descriptions: 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 ( email: cathryn.lewis@kcl.ac.uk), Douglas Levinson, Lesley Wise
- web/ftp: http://mmg.umds.ac.uk/GSMA
- source code language: C++
- operating systems: UNIX(Solaris), MS-DOS
- executables:
- reference:
Wise et al. (1999),
Annals of Human Genetics, 63:263-272.
Levinson et al., (2003), American Journal of Human Genetics, 73(1):17-33. [html]
- GTOOL
- full name:
- version: 0.4.1 (Feb 2008)
- descriptions: GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
- authors: Jonathan Marchini
- web/ftp: http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html
- source code language:
- operating systems:
- executables:
- reference:
H - HAP (1)
- full name: haplotype resolution using imperfect phylogeny
- version: 3.0
- descriptions:
- authors: Eleazar Eskin ( eeskin@cs.ucsd.edu )
- web/ftp:
http://research.calit2.net/hap/
http://www.cs.columbia.edu/compbio/hap/ - source code language:
- operating systems:
- executables:
- reference:
- HAP (2)
- full name: HAPlotype analysis of polymorphic markers
- version:
- descriptions:
- authors: (MRC Epidemiology Unit at Strangeways Research Lab, UK) (email: jinghua.zhao@mrc-epid.cam.ac.uk )
- web/ftp: http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/
- source code language: C
- operating systems: MS-Windows, UNIX(Solaris), Linux
- executables:
- reference: Zhao (2004), "2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis", Bioinformatics, 20:1325-1326.
- HAPAR
- full name: HAplotype inference by PARsimony
- version:
- descriptions: HAPAR is a program to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes.
- authors: Lusheng Wang (City University of Hong Kong), Ying Xu (Stanford Univ),
- web/ftp:
http://theory.stanford.edu/~xuying/hapar/
http://www.cs.cityu.edu.hk/~lwang/hapar/index.html - source code language:
- operating systems: MS-Window, UNIX(Solaris/..)
- executables:
- reference: Wang, Xu (2003), "Haplotype inference by maximum parsimony", Bioinformatics, 19(14):1773-1780.
- HAPASSOC
- full name:
- version:
- descriptions: a likelihood approach is used to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis' formula.
- authors:
- web/ftp: http://stat-db.stat.sfu.ca:8080/statgen/research/hapassoc
- source code language: R
- operating systems:
- executables:
- reference:
- HAPBLOCK
- full name: a dynamical programming algorithm for haplotype block partitioning
- version: 2002
- descriptions:
- authors: Kui Zhang, Fengzhu Sun (USC)
- web/ftp: http://www-hto.usc.edu/msms/HapBlock/
- source code language: C
- operating systems: MS-Windows, Linux, UNIX(Solaris)
- executables:
- reference:
Kui Zhang, Minghua Deng, Ting Chen, Michael S Waterman, Fengzhu Sun
(2002),
Proceddings of the National Academy of Sciences , 99:7335-7339.
Zhang, Qin, Chen, Liu, Waterman, Sun (2005), "HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms", Bioinformatics, 21(1):131-134.
- HAPBLOCK (2)
- full name:
- version: April 2004
- descriptions:
- authors: Adrian Paul Mander (Boston College) (email: adrian.mander@mrc-hnr.cam.ac.uk)
- web/ftp: http://econpapers.repec.org/software/bocbocode/s438902.htm
- source code language: Stata
- operating systems:
- executables:
- reference:
- HAPGEN
- full name:
- version: 1.3.0 (Jan 2008)
- descriptions: HAPGEN is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region. The disease model is specified through the choice of a single SNP as the disease causing variant together with the relative risks of the genotypes at the disease SNP. The program is designed to work with publically available files that contain the haplotypes estimated as part of the HapMap project and the estimated fine-scale recombination map derived from that data. Hapgen is computationally tractable. On a modern desktop HAPGEN can simulate several thousand case and control data on a whole chromosome at Hapmap Phase 2 marker density within minutes. This program has been used to assess the power of several different commercially available genotyping chips, in the design stage of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) and for evaluating the power of different methods for detecting association in genome-wide studies.
- authors: Zhan Su, Jonathan Marchini, Peter Donnelly (Univ of Oxford, UK)
- web/ftp: http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html
- source code language: C++
- operating systems:
- executables:
- reference:
- HAPINFERX
- full name:
- version: (Jul 1999)
- descriptions:
- authors: Andrew Clark (email: ac347@cornell.edu)
- web/ftp: (temporary) source code , input example file , output example file
- source code language: FORTRAN
- operating systems:
- executables:
- reference: Clark (1990), "Inference of haplotype from PCR-amplified samples of diploid populations", Molecular Biology and Evolution, 7:111-122.
- HAPLO (1)
- full name: Haplotyping with computation of conditional probabilities
- version 1.00 (feb 5, 1996)
- descriptions: assigns each person the haplotype with the highest conditional probability using Elston-Stewart algorithm
- authors: Daniel E. Weeks (Pittsburgh) and Kenneth Lange (UCLA) (Collaborators: Jeffrey R O'Connell and Eric Sobel)
- web/ftp:
http://watson.hgen.pitt.edu/register/soft_doc.html,
registration page at: http://watson.hgen.pitt.edu/register - source code language: Fortran 77 (ANSI standard)
- operating systems: UNIX (SunOS/Solaris/HP)
- executables:
- reference:
Sobel, Lange, O'Connell and Weeks, in
"Genetic Mapping and DNA Sequencing"
(IMA Volumes in Mathematics and its Applications)
eds. T.P. Speed and M.S. Waterman (Springer-Verlag, 1995).
Weeks, Sobel, O'Connell, Lange (1995), American Journal of Human Genetics, 56(6):1506-1507. [abstract]
- HAPLO (2)
- full name:
- version: 2.5 (1998)
- descriptions: Estimates frequencies of multi-site haplotypes using the EM algorithm
- authors: ME Hawley, KK Kidd
- web/ftp: http://krunch.med.yale.edu/haplo/
- source code language: FORTRAN
- operating systems: DEC VAX
- executables:
- reference: Hawley, Kidd (1995), "HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes", Journal of Heredity, 86:409-411.
- HAPLOBLOCK
- full name:
- version: 1.2 (April 28, 2004)
- descriptions: HAPLOBLOCK is a software package which provides an integrated approach to haplotype block identification, haplotype resolution and linkage disequilibrium mapping, suitable for high-density phased or unphased SNP data.
- authors: Gideon Greenspan (web/ftp: http://www.gidgreen.com/ ) Dan Geiger (web/ftp: http://www.cs.technion.ac.il/people/dang/)
- web/ftp: http://bioinfo.cs.technion.ac.il/haploblock/
- source code language: C
- operating systems: UNIX(Solaris), Linux, MacOS X
- executables: haploblock_b, haploblock_n
- reference:
Greenspan, Geiger (2004),
"Model-based inference of haplotype block variation",
Journal of Computational Biology, 11(2-3):493-504.
Greenspan, Geiger (2004), "High density linkage disequilibrium mapping using models of haplotype block variation", Bioinformatics, 20(1):137-144.
Instruction Manual: http://bioinfo.cs.technion.ac.il/haploblock/HaploBlock_Manual.pdf
LD Mapping Supplement http://bioinfo.cs.technion.ac.il/haploblock/HaploBlock_Mapping.pdf
- HAPLOBLOCKFINDER
- full name:
- version: 0.7
- descriptions: HaploBlockFinder is a package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine.
- authors: Kun Zhang (kun.zhang@uth.tmc.edu)
- web/ftp: http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi
- source code language: C and Perl
- operating systems: UNIX, MS-Windows
- executables: haploBlockFinder, hbfWrapper.pl, showLDmatrix.pl, drawBlocks.pl
- reference:
- HAPLOBUILD
- full name:
- version:
- descriptions: The analysis of large amounts of SNP data creates difficulties for the analysis of haplotypes and their association to traits of interest. Commonly fairly simple methods, such as two- or three-SNP sliding windows are used to create haplotypes across large regions, but these may be of limited value when adjacent SNPs are in strong LD and provide redundant information. We have created a novel program, "HaploBuild" for constructing and testing haplotypes for SNPs in close physical proximity to one another but which are not necessarily contiguous. Furthermore, the number of SNPs contained in the haplotype is not restricted, thereby permitting the evaluation of complex haplotype structures.
- authors: JM Laramie, JB Wilk, AL DeStefano, RH Myers (Boston University)
- web/ftp: http://snp.bumc.bu.edu/modules.php?name=HaploBuild
- source code language: Perl
- operating systems: Linux, MS-Windows, MacOS
- executables:
- reference: Laramie, Wilk, DeStefano, Myers (2007), "HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies", Bioinformatics, 23(16):2190-2192.
- HAPLOCLUSTERS
- full name:
- version:
- descriptions: a program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population.
- authors: Melanie Bahlo (email: bahlo@wehi.edu.au)
- web/ftp: http://bioinf.wehi.edu.au/folders/melanie/haploclusters.html
- source code language:
- operating systems:
- executables:
- reference: Bahlo,Stankovich,Speed,Rubio,Burfoot,Foote (2006), "Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data", Human Genetics, 119(1-2):38-50.
- HAPLOPAINTER
- full name:
- version: 0.027b
- descriptions: A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK
- authors: Holger Thiele, Peter Nuernberg (Max-Delbruck-Centrum fur Molekulare Medizin, Berlin-Buch).
- web/ftp: http://haplopainter.sourceforge.net/html/ManualIndex.htm
- source code language: Perl
- operating systems:
- executables:
- reference: Thiele, Nurnberg (2005), "HaploPainter: a tool for drawing pedigrees with complex haplotypes", Bioinformatics, 21(8):1730-1732.
- HAPLOPOOL
- full name:
- version:
- descriptions: HaploPool is a program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4.
- authors:
- web/ftp: http://haplopool.icsi.berkeley.edu/haplopool/
- source code language: gcc/g++, perl, MATLAB
- operating systems:
- executables:
- reference: Kirkpatrick, Santos-Armendariz, Karp, Halperin (2007), "HaploPool: improving haplotype frequency estimation through DNA pools and phylogenetic modeling", Bioinformatics, 23(22):3048-3055.
- HAPLORE
- full name: HAPLOtype REconstruction in pedigrees
- version:
- descriptions: haplotype reconstruction in general pedigree without recombination
- authors: Hongyu Zhao (Yale, email: hongyu.zhao@yale.edu)
- web/ftp: http://bioinformatics.med.yale.edu/group/software.html
- source code language:
- operating systems:
- executables:
- reference: Zhang, Sun, Zhao (2005), "HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination", Bioinformatics, 21(1):90-103.
- HAPLOREC
- full name:
- version: 2.0
- descriptions: population-based haplotyping
- authors:
- web/ftp: http://www.cs.helsinki.fi/group/genetics/haplotyping.html
- source code language:
- operating systems:
- executables:
- reference: Eronen, Geerts, Toivonen (2004), "A Markov Chain Approach to Reconstruction of Long Haplotypes", Pacific Symposium on Biocomputing, 9:104-115.
- HAPLO.STAT (previously HAPLO.SCORE )
- full name:
- version: 1.2.0 (2005)
- descriptions: A suite of routines for the analysis of indirectly measured haplotypes.
- authors: Dan Schaid, Jason Sinnwell, Charles Rowland, David Tines (Mayo Clinic)
- web/ftp: http://mayoresearch.mayo.edu/mayo/research/biostat/schaid.cfm
- source code language: S-plus 6.1.2, R 1.7.1
- operating systems: UNIX
- executables: haplo.em, haplo.glm, haplo.score
- reference: Schaid, Rowland, Tines, Jacobson, Poland (2002), American Journal of Human Genetics, 70(2)(2):425-434. [html]
- HAPLOT
- full name:
- version: 2.5 (March 1998)
- descriptions: A simple program for graphical presentation of haplotype block structures, tagSNP selection and SNP variation.
- authors:
- web/ftp: http://info.med.yale.edu/genetics/kkidd/programs.html
- source code language: FORTRAN
- operating systems: VMS
- executables:
- reference: Gu, Pakstis, Kidd (2005), "HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations", Bioinformatics, 21:3938-3939.
- HAPLOTTER
- full name:
- version:
- descriptions: HAPLOTTER is a web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. It can be used as a resource to examine various population genetic measures in a genomic region. Measures that are currently displayed include iHS (a statistic developed to detect recent positive selection), Fay and Wu's H, Tajima's D and Fst.
- authors: S. Kudaravalli, X.Wen, J.K.Pritchard (email: pritch@uchicago.edu) (Univ of Chicago)
- web/ftp: http://hg-wen.uchicago.edu/selection/haplotter.htm
- source code language:
- operating systems: web-based
- executables:
- reference: Voight, Kudaravalli, Wen, Pritchard (2006), "A map of recent positive selection in the human genome", PLoS Biology, 4(3):e72.
- HAPLOTYPE ESTIMATION
- full name:
- version:
- descriptions: The haplotype estimation service is available in two variants: one for genetic data from unrelated probands (e.g., case/control studies) and one for core family data
- authors: K Rohde, R Furst (MDC Berlin)
- web/ftp: http://www.bioinf.mdc-berlin.de/projects/hap/
- source code language:
- operating systems:
- executables:
- reference: K Rohde, R Furst (2001), "Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information", Human Mutation, 17(4):289-295.
- HAPLOTYPER
- full name:
- version:
- descriptions:
- authors: T Niu, Jun Liu (Harvard Univ)
- web/ftp: http://www.people.fas.harvard.edu/~junliu/Haplo/docMain.htm
- source code language:
- operating systems:
- executables:
- reference: Niu, Qin, Xu, Liu (2002), "Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms", American Journal of Human Genetics, 70(1):157-169. [html]
- HAPLOVIEW
- full name:
- version: 3.32 (May 2006)
- descriptions: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable.
- authors: Jeffrey Barrett (Whitehead Institute)
- web/ftp: http://www.broad.mit.edu/personal/jcbarret/haploview/
- source code language: Java
- operating systems:
- executables:
- reference: Barrett, Fry, Maller, Daly (2005), "Haploview: analysis and visualization of LD and haplotype maps", Bioinformatics, 21(2):263-265.
- HAPLOVISUAL
- full name:
- version:
- descriptions:
- authors: Esko Ukkonen, Pasi Rastas
- web/ftp: http://www.cs.helsinki.fi/u/prastas/haplovisual/
- source code language: java
- operating systems:
- executables:
- reference: Ukkonen (2002), "Finding founder sequences from a set of recombinants" Lecture Notes in Computer Science Vol 2452, pp.277-286 (Springer).
- HAPLOWSER
- full name: HAPLotype brOWSER
- version:
- descriptions:
- authors:
- web/ftp: http://embio.yonsei.ac.kr/haplowser/
- source code language: Java
- operating systems:
- executables:
- reference: Kim, Kim, Waterman, Park, Li (2009), "HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome", Bioinformatics, 25(18):2430-2431.
- HAPMINER
- full name:
- version: 1.1 (2006)
- descriptions: HapMiner is a computer program for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions.
- authors: Jing Li (email:jingli@eecs.case.edu)
- web/ftp: http://vorlon.case.edu/~jxl175/HapMiner.html
- source code language:
- operating systems: MS-Windows, Linux
- executables:
- reference: Li and Jiang (2005), "Haplotype-based linkage disequilibrium mapping via direct data mining", Bioinformatics, 21(24):4384-4393.
- HAPMIXMAP
- full name:
- version:
- descriptions: HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program.
- authors: Paul McKeigue (email: paul.mckeigue@ucd.ie), David O'Donnell (University College Dublin, Ireland)
- web/ftp: http://www.ucd.ie/genepi/hapmixmap/hapmixintro.html
- source code language:
- operating systems:
- executables:
- reference:
- HAPPY
- full name: reconstructing HAPlotYpes
- version:
- descriptions: a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals
- authors: Richard Mott (Wellcome Trust Centre for Human Genetics, UK. rmott@well.ox.ac.uk )
- web/ftp: http://www.well.ox.ac.uk/~rmott/happy.html
- source code language: ANSI C (requires NAG C library)
- operating systems: UNIX(IRIX,SunOS), Linux
- executables:
- reference:
- HAP-SAMPLE
- full name:
- version:
- descriptions: HAP-SAMPLE is a web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be "genotyped," along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.
- authors:
- web/ftp: http://www.hapsample.org/
- source code language:
- operating systems: web-based
- executables:
- reference: Wright, Huang, Guan, Gamiel, Jeffreis, Barry, Pardo-Manuel, Sullivan, Wilhelmsen, Zou (2007), "Simulating association studies: a data-based resampling method for candidate regions or whole genome scans", preprint.
- HAPSCOPE
- full name:
- version:
- descriptions: HapScope includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes.
- authors: Jinghui Zhang (National Cancer Institute, NIH)
- web/ftp: http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/
- source code language:
- operating systems:
- executables:
- reference: Zhang, Rowe, Struewing, Buetow (2002), "HapScope: a software system for automated and visual analysis of functionally annotated haplotypes", Nucleic Acid Research, 30:5213-5221.
- HAPSIMU
- full name:
- version:
- descriptions: HAPSIMU is based on real haplotype data from the HapMap ENCODE project. This platform can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users.
- authors: Feng Zhang, Hong-Wen Deng
- web/ftp: http://l.web.umkc.edu/liujian/
- source code language: C++
- operating systems:
- executables:
- reference: Zhang, Liu, Chen, Deng (2008), "HAPSIMU: a genetic simulation platform for population-based association studies", BMC Bioinformatics, 9:331.
- HAPSTAT
- full name:
- version:
- descriptions: HAPSTAT is a user-friendly software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. The current version considers cross-sectional, case-control and cohort studies.
- authors: Danyu Lin, Donglin Zeng (email: linsoft@bios.unc.edu)
- web/ftp: http://www.bios.unc.edu/~lin/hapstat/
- source code language:
- operating systems: MS-Windows(XP/2000/NT/98)
- executables:
- reference:
Lin, Zeng, Millikan (2005), "Maximum likelihood estimation of haplotype
effects and haplotype-environment interactions in association studies",
Genetic Epidemiology, 29:299-312.
Lin, Zeng (2006), "Likelihood-based inference on haplotype effects in genetic association studies (with discussion)", Journal of American Statistical Association, 101:89-118.
Zeng, Lin, Avery, North, Bray (2006), "Efficient semiparametric estimation of haplotype-disease associations in case-cohort and nested case-control studies", Biostatistics, 7(3):486-502.
- HARDY (see also PANGAEA)
- full name:
- version: July 1996
- descriptions: Markov chain Monte Carlo program for association in two-dimensional contingency tables, and for testing Hardy-Weinberg equilibrium.
- authors: Sun-Wei Guo (U. Minnesota,
guo_s@epivax.epi.umn.edu
E.A. Thompson (Univ Washington) - web/ftp: http://www.stat.washington.edu/thompson/Genepi/Hardy.shtml
- source code language: C
- operating systems: UNIX(DEC-UNIX/..)
- executables:
- reference: Guo and Thompson (1992), Biometrics, 48, 361-372.
- HCLUST.R
- full name:
- version:
- descriptions: a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data
- authors:
- web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/hclust.htm
- source code language: R
- operating systems:
- executables:
- reference:
- HEGESMA
- full name: HEterogeneity and GEnome Search Meta Analysis
- version:
- descriptions: HEGESMA is a comprehensive software for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels.
- authors: Elias Zintzaras, (email: zintza@med.uth.gr) John PA Ioannidis
- web/ftp: http://biomath.med.uth.gr
- source code language:
- operating systems:
- executables:
- reference: Zintzaras, Ioannidis (2005), "HEGESMA: genome search meta-analysis and heterogeneity testing", Bioinformatics, 21(18):3672-3673.
- HELIXTREE
- full name: HelixTree Genetic Association Software
- version: 6
- descriptions: Comprehensive toolset for population-based association studies. Perform allele, genotype, haplotype, multi-locus, runs of homozygosity, copy number variation, and regression-based association analysis on case-control, quantitative trait, and categorical type data.
- authors: Christophe Lambert, Dmitri Zaykin, Douglas Hawkins, Stanley Young, Alan Menius, Meg Ehm, Mike Mosteller
- web/ftp:
http://www.goldenhelix.com/SNP_Variation/HelixTree
Download request for free trial available at http://www.goldenhelix.com/SNP_Variation/svstrial.html - source code language: C++
- operating systems: MS-Windows, Linux, MacOS X
- executables: helixtree.exe
- reference:
Zaykin, Westfall, Young, Karnoub, Wagner, Ehm (2002),
"Testing association of statistically inferred haplotypes with
discrete and continuous traits in samples of unrelated individuals",
Human Heredity, 53:79-91.
Recursive Partitioning, A Bibliography http://www.goldenhelix.com/download/pdfs/RPbibliography.pdf
- price: Academic pricing available. Please contact Golden Helix, Inc. at info@goldenhelix.com
- HIT
- full name: Haplotype Inference Technique
- version:
- descriptions:
- authors: Pasi Rastas
- web/ftp: http://www.cs.helsinki.fi/u/prastas/hit/
- source code language: java
- operating systems:
- executables:
- reference:
Rastas, Koivisto, Mannila, Ukkonen (2005),
"A Hidden Markov Technique for Haplotype Reconstruction",
5th Workshop on Algorithms in Bioinformatics - WABI 2005
Rastas, Koivisto, Mannila, Ukkonen (2008), "Phasing genotypes using a hidden Markov model", in eds. I Mandoiu and A Zelikovsky, Bioinformatics Algorithms: Techniques and Applications, pp. 373-391 (Wiley).
- HOMOG/HOMOGM
- full name:
- version: HOMOGM: Dec 1998
- descriptions:
- authors: Jurg Ott (Columbia Univ)
- web/ftp:
ftp://linkage.rockefeller.edu/software/homog ;
ftp://linkage.rockefeller.edu/software/homogm - source code language: Pascal, C (homogm)
- operating systems:
- executables: homog, homog1a, homog1b, homog2, homog3, homog4, homog3r, point4, mtest
- reference:
Ott (1986),
Genetic Epidemiology, Suppl,1,251-257.
online documentation
- HOTSPOTTER
- full name:
- version: 1.2.1
- descriptions: Hotspotter implements the PAC (Products of Approximate Conditional) model for estimating recombination rate
- authors: Na Li
- web/ftp: http://www.biostat.umn.edu/~nali/SoftwareListing.html
- source code language: C++
- operating systems:
- executables: rholike, hotspot, fullopt
- reference: Li, Stephens (2003), Genetics, 165(4):2213-2233.
- HPLUS
- full name:
- version: 2.5
- descriptions: HPlus is an analysis tool for performing haplotype estimation on genetic markers such as SNPs and microsatellites. It is able to handle datasets that include case-control status as well as covariates and marker location variables (such as gene name, chromosome location, etc).
- authors: Sue Li, RJ Laws, LuePing Zhao (Fred Hutchinson Cancer Research Center)
- web/ftp: http://cougar.fhcrc.org/hplus/
- source code language:
- operating systems: MS-Windows, Linux
- executables:
- reference:
Zhao, Li, Khalid (2003),
"A method for assessing disease associations with SNP
haplotypes and environmental variables in case-control",
American Journal of Human Genetics, 72(5):1231-1250.
[html]
Li, Khalid, Carlson, Zhao (2003), "Estimating haplotype frequencies and standard errors for multiple single nucleotide polymorphisms", Biostatistics, 4:513-522.
- HS-TDT
- full name: Haplotype Sharing Transmission Disequilibrium Test
- version:
- descriptions: testing association using tightly linked markers in nuclear pedigrees
- authors: Shuanglin Zhang (email: shuzhang@mtu.edu)
- web/ftp: http://www.math.mtu.edu/~shuzhang/software.html
- source code language:
- operating systems: UNIX, MS-Windows
- executables:
- reference:
Zhang, Sha, Chen, Dong, Jiang (2003),
"Transmission/disequilibrium test based on haplotype sharing for
tightly linked markers",
American Journal of Human Genetics, 73(3):566-579.
[html]
Zhang, Sha, Chen, Dong, Jiang (2004), "Impact of genotyping error on type I error rate of the haplotype-sharing transmission /disequilibrium test (HS-TDT): reply to Knapp and Becker" (letter), American Journal of Human Genetics, 74(3):591-593. [html]
- HTR
- full name: Haplotype Trend Regression
- version: Aug 2002
- descriptions: Haplotype association mapping using unrelated individuals; "fixed" and "sliding" window analysis; overall tests and tests for individual haplotype effects
- authors: Dmitri Zaykin
- web/ftp:
http://statgen.ncsu.edu/zaykin/htr.html
ftp://statgen.ncsu.edu/pub/zaykin/htr/ - source code language: C++, Bash shell
- operating systems: Window, UNIX(Solaris)
- executables: emgi.exe (fixed number of markers), bash emgi.sh (sliding window)
- reference: Zaykin DV, Westfall PH, Young SS, Karnoub MC, Wagner MJ, Ehm MG (2002), "Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals", Human Heredity, 53:79-91.
- HTSNPER
- full name: Haplotype Tagging SNPer
- version: 1.0 (Dec 2003)
- descriptions: htSNPer is a Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP
- authors: Keyue Ding, Jing Zhang (email: zhjing98@mails.tsinghua.edu.cn), Kaixin Zhou, Yan Shen, Xuegong Zhang (Tsinghua University, China)
- web/ftp: http://www.chgb.org.cn/htSNPer/htSNPer.html
- source code language: C++, JVM
- operating systems: MS-Windows, Linux
- executables:
- reference:
- HWMET
- full name:
- version:
- descriptions: Bayesian estimation of the population inbreeding coefficient f
- authors: KL Ayres (email: k.l.ayres@reading.ac.uk)
- web/ftp: http://www.reading.ac.uk/Statistics/genetics/software.html
- source code language: C
- operating systems:
- executables:
- reference:
- HWESTRATA
- full name:
- version:
- descriptions: Calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum.
- authors: Daniel Schaid (Mayo Clinic) (email: schaid@mayo.edu)
- web/ftp: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
- source code language: C
- operating systems: UNIX(Solaris), MS-Windows(XP)
- executables:
- reference:
I - IBDREG
- full name:
- version: 0.1.0 (December 2006)
- descriptions: A package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree.
- authors: Jason Sinnwell (email: sinnwell@mayo.edu), Daniel Schaid (Mayo Clinic)
- web/ftp: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
- source code language: R/S-PLUS
- operating systems:
- executables:
- reference:
- IGG
- full name: Integrate Genotypes for genome-wide Genetic studies
- version: 3.0
- descriptions: IGG is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators' projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.
- authors: Miao-Xin Li (email: limx54@163.com)
- web/ftp: http://bioinfo.hku.hk:13080/iggweb/
- source code language: Java
- operating systems: web-based
- executables:
- reference:
Li, Jiang, Ho, Song, Sham (2007),
"IGG: A tool to integrate GeneChips for genetic studies",
Bioinformatics, 23(22):3105-3107.
Li, Jiang, Kao, Sham, Song (2009), "IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis", Bioinformatics, 25(11):1449-1450.
- ILR
- full name: Imprinting Likelihood Ratio
- version: 2.2 (November 2005)
- descriptions: calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting
- authors: Michael Knapp (Univ Bonn) and Konstantin Strauch (Univ Marburg)
- web/ftp: http://www.uni-bonn.de/~umt70e/soft.htm
- source code language: SAS macro
- operating systems:
- executables:
- reference: Knapp, Strauch (2004), "Affected-sib-pair test for linkage based on constraints for identical-by-descent distributions corresponding to disease models with imprinting", Genetic Epidemiology, 26:273-285 (Erratum: 28:288).
- IMPUTE
- full name:
- version: 0.4.2 (June 2008)
- descriptions: IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes). The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO and HAPGEN and produce output that can be analyzed using the program SNPTEST. This program was used to carry out genotype imputation as part of the analysis of the 7 genome-wide association studies analyzed by the Wellcome Trust Case-Control Consortium (WTCCC)
- authors: Jonathan Marchini (email: marchini@stats.ox.ac.uk)
- web/ftp: http://www.stats.ox.ac.uk/~marchini/software/gwas/impute.html
- source code language:
- operating systems:
- executables:
- reference: Marchini, Howie, Myers, McVean, Donnelly (2007), "A new multipoint method for genome-wide association studies via imputation of genotypes", Nature Genetics, 39:906-913.
- INSEGT (see also PANGAEA)
- full name: INference of SEGregation Types
- version: 1.1 (September 1999)
- descriptions: the program constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree.
- authors: Jochen Kumm (email: jochen@u.washington.edu)
- web/ftp: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml
- source code language: C++ (the standard template library, STL, is used)
- operating systems:
- executables:
- reference:
- INTEGRAYEDMAP
- full name:
- version:
- descriptions: IntegratedMap is a web application and database schema for storing and interactively displaying genetic map data.
- authors: Hongyu Yang, Hongyu Wang, Alan Gingle (Center for Applied Genetic Technologies, University of Georgia)
- web/ftp: ftp://cggc.agtec.uga.edu/IntegratedMap/
- source code language:
- operating systems: MS-Windows (NT/2000/XP profession/), require either Oracle RDBMS or MySQL.
- executables:
- reference: Yang, Wang, Gingle (2005), "IntegratedMap: a web interface for integrating genetic map data", Bioinformatics, 21(9):2126-2127.
- INTERSNP
- full name:
- version: 1.0.4 (March 2010)
- descriptions: INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information).
- authors: Christine Herold, Tim Becker
- web/ftp: http://intersnp.meb.uni-bonn.de/
- source code language: C/C++
- operating systems: UNIX, MS-Windows, MacOS
- executables:
- reference: Herold, Steffens, Brockschmidt, Baur, Becker (2009), "INTERSNP: genome-wide interaction analysis guided by a priori information", Bioinformatics, 25(24):3275-3281
J - JENTI
- full name:
- version:
- descriptions: An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way.
- authors:
- web/ftp: http://www.jenti.org
- source code language: Java
- operating systems:
- executables:
- reference: Falchi, Fuchsberger (2008), "Jenti: an efficient tool for mining complex inbred genealogies", Bioinformatics, 24(5):724-726.
- JLIN
- full name: a Java based LINkage disequilibrium plotter
- version: 1.5.2 (March 2006)
- descriptions: JLIN (Java LINkage disequilibrium plotter) is designed for customisable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q.
- authors: Kim W Carter (Univ of Western Australian), Pamela A. McCaskie, Lyle J Palmer
- web/ftp: http://www.genepi.org.au/jlin
- source code language: Java
- operating systems: Any with Java 1.5 support
- executables: Java-based installer available from website
- reference: Carter, McCaskie, Palmer (2006), "JLIN: A java based linkage disequilibrium plotter", BMC Bioinformatics, 7:60.
- JOINMAP
- full name: Software for the calculation of genetic linkage maps
- version: 4 (October 2006)
- descriptions: Construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine ('join') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface.
- authors: Johan W Van Ooijen, Roeland E Voorrips (Plant Research International, Biometris, Wageningen, Netherlands) (email: mapping@biometris.nl)
- web/ftp: http://www.joinmap.nl/
- source code language: ANSI C, Delphi
- operating systems: MS-Windows (95/98/ME/NT4.0/2000)
- executables:
- reference: JW Van Ooijen, RE Voorrips (2001), "JoinMap (tm) 3.0: Software for the calculation of genetic linkage maps", Plant Research International, Wageningen, Netherlands; Stam (1993), The Plant Journal, 3, 739-744.
- J/QTL
- full name:
- version:
- descriptions: J/QTL is a Java GUI for the popular QTL data analysis software R/QTL. It provides a flexible and powerful working environment for users to perform a variety of tasks.
- authors: Hao Wu and Lei Wu (Jackson Lab) (email: jqtl@jax.com)
- web/ftp: http://www.jax.org/staff/churchill/labsite/software/Jqtl/index.html
- source code language: Java
- operating systems:
- executables:
- reference:
K - KIN
- full name:
- version: 1.05 (Dec 1995)
- descriptions: calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent)
- authors: Nick A. Tinker ( tinker@em.agr.ca ), Diane Mather (grain crops breeding and genetic research, McGill Univ, mather@agradm.lan.mcgill.ca)
- web/ftp:
http://gnome.agrenv.mcgill.ca/tinker/kin.htm
ftp://gnome.agrenv.mcgill.ca/software/KIN/ - source code language:
- operating systems: MS-DOS
- executables:
- reference: Tinker and Mather, Journal of Heredity, 84, 238 (1993)
L - LAMARC
- full name: Likelihood Analysis with Metropolis Algorithm using Random Coalescence
- version: 2.0.2 (August 2005)
- descriptions: The LAMARC program estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data.
- authors: Mary Kuhner, Jon Yamato, Peter Beerli (email: lamarc@gs.washington.edu)
- web/ftp: http://evolution.genetics.washington.edu/lamarc/lamarc_prog.html
- source code language: C++
- operating systems: Linux, MS-Windows, MacOS
- executables: lamarc, migrate, coalesce, fluctuate, recombine
- reference:
- LAMBDAA
- full name:
- version:
- descriptions:
- authors: AP Morris (email: amorris@well.ox.ac.uk)
- web/ftp: http://www.reading.ac.uk/Statistics/genetics/software.html
- source code language:
- operating systems:
- executables:
- reference: Morris, Whittaker, Curnow (1997), "A likelihood ratio test for detecting patterns of disease-marker association", Annals of Human Genetics, 61:335-350.
- LAMP
- full name: Linkage and Association Modeling in Pedigrees
- version: 0.0.7
- descriptions: LAMP carries out parametric association analysis in samples of unrelated individuals, trios or large families. In addition to a test-statistic, a genetic model is estimated for each SNP. The approach is based on retrospective likelihood and can be used to analyze selected samples.
- authors: Goncalo Abecasis (email: goncalo@umich.edu) and Mingyao Li
- web/ftp: http://www.sph.umich.edu/csg/abecasis/LAMP/download
- source code language: C++
- operating systems: UNIX, LINUX, MS-Windows, MacOS
- executables: lamp
- reference:
Li, Boehnke, Abecasis (2006),
"Efficient study designs for test of genetic association using
sibship data and unrelated cases and controls",
American Journal of Human Genetics, 78(5):778-792.
[html]
Li, Boehnke, Abecasis (2005), "Joint Modeling of Linkage and Association: Identifying SNPs Responsible for a Linkage Signal", American Journal of Human Genetics, 76(6):934-949. [html]
- LAPSTRUCT
- full name: LAPlacian eigenfunctions learn population STRUCTure
- version:
- descriptions: LAPSTRUCT is a free program to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1)geometrically motivated and graphic model based; (2)robustness of outliers.
- authors: Jun Zhang, P Niyogi, MS McPeek
- web/ftp: http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html
- source code language: R
- operating systems:
- executables:
- reference: Zhang, Niyogi, McPeek (2009), "Laplacian eigenfunctions learn population structure", PLoS ONE, 4(12):e7928.
- LCP
- full name: Linkage Control Program
- alias: LINKAGE/LCP
- version:
- descriptions: part of the LINKAGE auxiliary program
- authors: Peter Cartwright (Univ Utah, now Cimarron Software pc@cimsoft.com )
- web/ftp: ftp://linkage.rockefeller.edu/software/linkage or http://www.eurogene.org/portale/index.php?p=9_resources/resources.txt&l=en (please contact Alberto Goldoni, email: alberto.goldoni@eurogene.org if you have any questions on this version)
- source code language: C and Pascal
- operating systems: UNIX, VMS, MS-DOS, OS2
- executables:
- reference:
- LDA
- full name: Linkage Disequilibrium Analyzer
- version:
- descriptions: LDA is a Java program for analyzing the pairwise linkage disequilibrium.
- authors: Keyue Ding (email: keyued@chgb.org.cn), Kaixin Zhou, Fuchu He, Yan Shen
- web/ftp: http://www.chgb.org.cn/lda/lda.htm
- source code language: Java
- operating systems: MS-Windows, Linux, MacOS
- executables:
- reference: Ding, Zhou, He, Shen (2003), "LDA - A java-based linkage disequilibrium analyzer", Bioinformatics, 19:2147-2148.
- LDB/LDB+
- full name: Location DataBase
- version:
- descriptions: integrate genetic linkage map and physical map
- authors: A Collins ( arc@southampton.ac.uk), NE Morton, S. Lawrence, D. Shields, Jonathan Teague, Paul Linehan, Pietro Lio (University of Southampton, UK)
- web/ftp:
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ldb;
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ldb+ - source code language: FORTRAN
- operating systems: UNIX(SunOS/..)
- executables:
- reference:
Morton (1991),
Annals of Human Genetics, 55:235-241.
Morton, Collins, Lawrence, Shield (1992), Annals of Human Genetics, 56:223-232.
online manual and user guide
- LDGROUP
- full name:
- version: Nov 2007
- descriptions: inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.
- authors: Fumihiko Takeuchi (email: fumihiko@takeuchi.name)
- web/ftp: http://www.fumihiko.takeuchi.name/publications.html
- source code language: R
- operating systems:
- executables:
- reference: Takeuchi, Yanai, Morii, Ishinaga, Taniguchi-Yanai, Nagano, Kato (2005), "Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs", Genetics, 170:291-304.
- LDHAT