- QGENE
- full name:
- version: 4.0.2
- descriptions: A free, computationally effecient, easy-to-use Java program for comparative analyses of QTL mapping data and population simulation.
- authors: Roby Joehanes, Zhigang Guo, Prashanth Boddhireddy, J Clare Nelson (Kansas State University)
- web/ftp:
http://www.qgene.org/
http://coding.plantpath.ksu.edu/qgene/ - source code language: Java
- operating systems:
- executables:
- reference: Nelson (1997), "QGENE: software for marker-based genomic analysis and breeding", Molecular Breeding, 3:239-245. [abstract]
- QMSIM
- full name: Qtl and Marker SIMulator
- version: 1.0
- descriptions: QMSim was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.
- authors: Mehdi Sargolzaei (email: msargol@uoguelph.ca), Flavio S Schenkel
- web/ftp: http://www.aps.uoguelph.ca/~msargol/qmsim/
- source code language: C++
- operating systems: MS-Windows, Linux
- executables:
- reference: Sargolzaei, Schenkel (2009), "QMSim: a large-scale genome simulator for livestock", Bioinformatics, 25:680-681.
- QTDT
- full name: Quantitative (Trait) Transmission/Disequilibrium Test
- version: 2.5.1 (January 2005)
- descriptions: Performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation.
- Authors: Goncalo Abecasis (goncalo@well.ox.ac.uk)
- web/ftp: http://www.sph.umich.edu/csg/abecasis/QTDT/
- source code language: C++
- operating systems: UNIX(Solaris), Linux, MS-Windows
- executables: qtdt, prelude, finale, pedstats
- reference: Abecasis, Cardon and Cookson (2000), "A general test of association for quantitative traits in nuclear families", American Journal of Human Genetics, 66(1):279-292. [ html]
- QTL-ALL
- full name: QTL Analysis and Linkage Library
- version:
- descriptions: QTL-ALL is a software package designed to make as many as possible of the new statistics (e.g. score statistics) widely available. The software consists of a MEGA2-like interface for data analysis preparation and a library of R routines that computes linkage statistics. QTL-ALL reads in input data, creates re-formatted output data files, calls external IBD-generation software such as MERLIN or SIMWALK2, then computes statistics using our R library, and finally produces tables and plots of statistics and p-values. This entire sequence is highly automated, requiring minimal user-intervention. The initial release of the software computes a number of newer QTL-mapping statistics, including several score statistic variants, and can handle nuclear family data, including specialty designs such as discordant and concordant (affected) pairs.
- authors: Nandita Mukhopadhyay, S Bhattacharjee, CL Kuo, Dan Weeks, E Feingold
- web/ftp: http://watson.hgen.pitt.edu/register/
- source code language:
- operating systems:
- executables:
- reference: Am Soc Hum Genet annual meeting 2006 Mukhopadhyay, Bhattacharjee, Kuo, Weeks, Feingold, Am J Hum Genet, suppl. ?, ? (1995)). http://www.ashg.org/genetics/abstracts/abs06/f1567.htm
- QTL CAFE
- full name:
- version: May 1998
- descriptions: providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression.
- authors:
- web/ftp: http://www.biosciences-labs.bham.ac.uk/Kearsey/
- source code language:
- operating systems: Java
- executables:
- reference:
- QTL Cartographer
- full name:
- version: Window version 2.5 (September 2006)
- descriptions: A program to map quantitative traits sing a map of molecular markers.
- Authors: Christopher J. Basten, Bruce S. Weir, Zhao-Bang Zeng, Shengchu Wang (Dept Statistics, North Carolina State University);
- web/ftp:
http://statgen.ncsu.edu/qtlcart/cartographer.html
ftp://statgen.ncsu.edu/pub/qtlcart/ - source code language:
- operating systems: UNIX, MS-Windows, MacOS
- executables: rmap, rqtl, rcross, qstats, lrmapqtl, srmapqtl, zmapqtl, prune, preplot, eqtl, qtlcart
- reference:
Basten,Weir,Zeng (1994), "Zmap-a QTL cartographer",
in Proceedings of the 5th World Congress on Genetics Applied to
Livestock Production: Computing Strategies and Software,
vol 22, eds. Smith, Gavora, Chesnais, Fairfull, Gibson, Kennedy, Burnside.
online manual
- QTL EXPRESS
- full name:
- version: August 2005
- descriptions: A web-based user-friendly package to map Quantitative Trait Loci in outbred populations. Population structures catered for are line crosses, halfsib families, nuclear families and sibpairs. Permutation tests to determine empirical significance levels and bootstrapping to estimate empirical confidence intervals of QTL locations are optional. Fixed effects/covariates can be fitted and models may include single or multiple QTL. Results are presented in tabular and graphical format.
- authors: George Seaton (email: george.seaton@ed.ac.uk), Chris Haley, Sara Knott, Xijiang Yu, Peter Visscher (Institute of Cell, Animal and Population Biology, Univ. Edingbergh)
- web/ftp: http://qtl.cap.ed.ac.uk/
- source code language: Java
- operating systems: web-based
- executables:
- reference: G Seaton, CS Haley, SA Knott, M Kearsey, PM Visscher (2002), "QTL Express: mapping quantitative trait loci in simple and complex pedigrees", Bioinformatics, 18:339-340. [abstract]
- QTLNETWORK
- full name:
- version: 2.0
- descriptions: QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines.
- authors: Jian Yang, Chengcheng Hu, Xiuzi Ye, Jun Zhu (Zhejiang University)
- web/ftp: http://ibi.zju.edu.cn/software/qtlnetwork
- source code language:
- operating systems:
- executables:
- reference: Yang, Hu, Hu, Yu, Xia, Ye, Zhu (2008), "QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations", Bioinformatics. 24(5):721-723.
- QUANTO
- full name:
- version: 1.2.1 (January 2007)
- descriptions: 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. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents.
- authors: Jim Gauderman (email: jimg@usc.edu), John Morrison (email: jmorr@usc.edu)
- web/ftp: http://hydra.usc.edu/GxE
- source code language: C++
- operating systems: Window(98/NT/2000/..)
- executables: quanto.exe
- reference:
Gauderman (2002),
"Sample size requirements for matched case-control studies of
gene-environment interaction", Statistics in Medicine, 21:35-50.
[ abstract]
Gauderman (2002), "Sample size requirements for association studies of gene-gene interaction", American Journal of Epidemiology, 155:478-484. [abstract]
WJ Gauderman (2003), "Candidate gene association studies for a quantitative trait, using parent-offspring trios", Genetic Epidemiology, 25:327-338. [ abstract]
- QU-GENE
- full name: QUantitative GENEtics
- version: v1 (1998)
- descriptions: A package for quantitative analysis of genetic models
- Authors: D. Podlich (email: d.podlich@mailbox.uq.edu.au) and M. Cooper (email: m.cooper@mailbox.uq.edu.au)
- web/ftp: http://pig.ag.uq.edu.au/qu-gene/ (not available)
- source code language: Fortran
- operating systems: MS-Windows
- executables: qugene.exe
- reference: Podlich, Cooper (1998), "QU-GENE: a simulation platform for quantitative analysis of genetic models", Bioinformatics. 14:632-653. Online manual: http://pig.ag.uq.edu.au/qu-gene/manual.htm
- QUTIE (see also CCRAVAT )
- full name: Case-Control RAre Variant Analysis Tool
- version:
- descriptions: Enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design.
- authors: Eleftheria Zeggini's group (Wellcome Trust Sanger Institute)
- web/ftp: http://www.sanger.ac.uk/resources/software/rarevariant/
- source code language:
- operating systems:
- executables:
- reference:
R - RC-TDT
- full name: Reconstruction-Combined Transmission Disequilibrium Test
- version: 1.1d (Jul 2006)
- descriptions: A family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. The distribution contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values.
- authors: Michael Knapp (Univ Bonn)
- web/ftp: http://www.uni-bonn.de/~umt70e/soft.htm
- source code language: SAS macro
- operating systems:
- executables:
- reference:
Knapp (1999),
"The transmission/disequilibrium test and parental-genotype
reconstruction: the reconstruction-combined transmission/disequilibrium test",
American Journal of Human Genetics, 64(3):861-870.
[ abstract]
Knapp (1999b), "Using exact P values to compare the power between the reconstruction-combined transmission/disequilibrium test and the sib transmission/disequilibrium test" (letter), American Journal of Human Genetics, 65:1208-1210. [ html]
Horvath, Laird, Knapp (2000), "The transmission/disequilibrium test and parental-genotype reconstruction for X-chromosomal markers", American Journal of Human Genetics, 66(3):1161-1167. [ html]
- REAPER
- full name:
- version: 1.0
- descriptions: tag SNP selelciton tool according to r2-bins method. It is specifically designed for full genome scale deterministic tagging.
- authors: Reedik Magi, Lauris Kaplinski, Maido Remm (Univ of Tartu, Estonia)
- web/ftp: http://bioinfo.ebc.ee/download/
- source code language:
- operating systems: MS-Windows, Linux
- executables:
- reference: Magi, Kaplinski, Remm (2006), "The whole genome TagSNP selection and transferability among HapMap populations", Pacific Symposium on Biocomputing, 11:535-543.
- RECORD
)- full name: REcombination Counting and ORDering
- version: 2005 and 2006
- descriptions: RECORD can be used for the ordering of loci on genetic linkage maps. The method is based on minimisation of the total number of recombination events. Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Data files are .LOC JoinMap format. Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes.
- authors:
Piet Stam, Herman van Eck (Wageningen University,
Laboratory for Plant Breeding, email:
- web/ftp: http://www.plantbreeding.wur.nl/UK/software_record.html
- source code language: C++
- operating systems: MS-Windows (Win98, XP) and MS-DOS
- executables: record_win.exe, ord.exe
- reference: Van Os, Stam, Visser, Van Eck (2005), "RECORD: A novel method for ordering loci on a genetic linkage map", Theoretical and Applied Genetics, 112(1):30-40. [abstract]
Van Os, Andrzejewski, Bakker, Barrena, Bryan, Caromel, Ghareeb, Isidore, de Jong, van Koert, Lefebvre, Milbourne, Ritter, van der Voort, Rousselle-Bourgeois, van Vliet, Waugh, Visse, Bakke, Van Eck (2006), "Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map", Genetics, 173(2):1075-1087. [abstract]
- full name:
- version: 1.10 (dec 97)
- descriptions: software for relationship estimation, in particular between putative sibs when parents are untyped
- authors: Harald Göring (e-mail: hhg2@columbia.edu)
- web/ftp: ftp://linkage.rockefeller.edu/software/relative
- source code language: ANSI C
- operating systems: MS-DOS, MS-Windows, UNIX
- executables: relative
- reference:
Am Soc Hum Genet annual meeting 1995
(Göring and Ott, Am J Hum Genet, suppl. 57, A192 (1995));
Göring and Ott (1997), "Relationship estimation in affected sib pair analysis of late-onset diseases", European Journal of Human Geneics, 5:69-77.
- full name:
- version:
- descriptions: relativeFinder is a program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. Some of the unique features in relativeFinder are the batch mode options, that allow large jobs to be divided into many smaller jobs (suitable for deployment on a compute cluster environment), and the flexibility of the underlying Merlin engine, which allows relative finder to handle large pedigrees and consider a variety of alternate relationships -- including potential relationships specified by the user on the fly.
- authors: Abecasis's group (Univ Michigan)
- web/ftp: http://genome.sph.umich.edu/wiki/RelativeFinder
- source code language:
- operating systems:
- executables:
- reference:
- full name:
- version: 0.67 (August 2000)
- descriptions: Program for verifying the relationships between all pairs of individuals in a linkage study, by use of (autosomal) genome scan data, with allowance for the presence of genotyping errors.
- Authors: Karl W. Broman (Johns Hopkins Univ, kbroman@jhsph.edu)
- web/ftp: http://www.biostat.jhsph.edu/~kbroman/software/
- source code language: C
- operating systems: MS-DOS, MS-Windows, UNIX
- executables: relcheck
- reference:
Boehnke, Cox (1997),
"Accurate inference of relationships in sib-pair linkage studies",
American Journal of Human Genetics, 61(2):423-429.
[ abstract]
Broman, Weber (1998), "Estimation of pairwise relationships in the presence of genotyping errors" (letter), American Journal of Human Genetics, 63(5):1563-1564. [ abstract]
- full name:
- version: 2.01 (June 2004)
- descriptions: A program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample.
- Authors: Michael Boehnke, William Duren (Biostat, U Michigan)
- web/ftp: http://csg.sph.umich.edu/boehnke/relpair.php
- source code language: FORTRAN77
- operating systems: MS-Windows (95), UNIX
- executables:
- reference: Am Soc Hum Genet annual meeting 1997 (Duren,Cox,Hauser,Boehnke, Am J. Hum Genet. suppl 61, A273(1997)).
- full name:
- version:
- descriptions: a computer program for determining biological relatedness between individuals based on allele sharing at microsatellite loci
- authors: D.N. Stivers (dstivers@utsph.uth.tmc.edu), Y. Zhong, C.L. Hanis, R. Chakraborty (Univ of Texas at Houston)
- web/ftp: http://hgc.sph.uth.tmc.edu (not available yet)
- source code language:
- operating systems:
- executables:
- reference:
Chakraborty, Jin (1993),
"Determination of relatedness between individuals using DNA fingerprinting",
Human Biology, 65(6):875-895.
Am Soc Hum Genet annual meeting 1996 (Stivers, Zhong, Hanis, Chakraborty, Am J. Hum Genet. suppl 59, A190 (1996)).
- full name: Radiation Hybrid Map
- version: 3.0 (Sept 1996)
- descriptions:
- authors: Michael Boehnke (Univ Michigan, boehnke@sph.umich.edu),E. Hauser, K. Lange, K. Lunetta, J. Uro, J. VanderStoep
- web/ftp: http://csg.sph.umich.edu/boehnke/rhmap.php
- source code language: FORTRAN77
- operating systems:
- executables: rhmap, rh2pt, rhminbrk, rhmaxlik
- reference:
Boehnke,Lange,Cox (1991),
"Statistical methods for multipoint radiation hybrid mapping",
American Journal of Human Genetics, 49(6):1174-1188.
[ abstract]
Lange,Boehnke, Cox, Lunetta (1995), Genome Research, 5:136-150.
Lunetta,Boehnke, Lange, Cox (1995), Genome Research, 5:151-163.
- full name:
- version: 1.22 (1998)
- descriptions: an interactive program for radiation hybrid mapping
- authors: Lincoln Stein (Whitehead Institute, lstein@genome.wi.mit.edu)
- web/ftp:
http://www-genome.wi.mit.edu/ftp/pub/software/rhmapper/
ftp://ftp-genome.wi.mit.edu/pub/software/rhmapper - source code language: Perl
- operating systems:
- executables:
- reference:
Hudson, Stein, et al. (1995),
Science, 270:1945-1954.
Slonim, Stein, Kruglyak, Lander (1996), in preparation.
online user's guide
- full name: RISk CALculation in Windows
- version:
- descriptions: RISCALW is a novel convenient Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account.
- authors: Christine Fischer (email: christine.fischer@med.uni-heidelberg.de)
- web/ftp: http://www.riscalw.uni-hd.de
- source code language: Delphi 4
- operating systems: MS-Windows
- executables:
- reference:
Fischer, Kruger, Gross (2006),
"RISCALW: a windows program for risk calculation
in families with Duchenne Muscular Dystrophy",
Annals of Human Genetics, 70:249-254.
Fischer, Gross, Kruger, Cremer, Vogel, Grimm (2006), "Modeling germline mosaicism and different new mutation rates simultaneously for appropriate risk calculations in families with Duchenne muscular dystrophy", Annals of Human Genetics, 70:237-248.
- full name: Regression of Offspring on Mid-Parent (REVised)
- version: 0.2.1beta
- descriptions: a software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data.
- authors: Marie-Helene Roy-Gagnon and Alexander F. Wilson (afw@mail.nih.gov)
- web/ftp:
http://research.nhgri.nih.gov/ROMPrev/
ftp://ftp.nhgri.nih.gov/pub/software/ROMPrev/ - source code language: R
- operating systems: any with R installation
- executables:
- reference:
Roy-Gagnon, Mathias, Fallin, Jee, Broman, Wilson (2008),
"An extension of the Regression of Offspring on Mid-Parent to test for
association and estimate locus-specific heritability: The revised ROMP method",
Annals of Human Genetics, 72:115-125.
Roy-Gagnon (2004), "Theoretical and applied investigations of a Regression of Offspring on Mid-Parent approach: Familial idiopathic scoliosis", Ph.D. dissertaion. Johns Hopkins University.
Pugh, Papanicolaou, Justice, Roy-Gagnon, Sorant, Kingman, Wilson (2001), "Comparison of variance components, ANOVA and regression of offspring on midparent (ROMP) methods for SNP markers", Genetic Epidemiology, 21(Suppl 1):S794-S799.
- full name:
- version: evaluation version (October 2007)
- descriptions: The Rosetta Syllego system is a genetic data management and analysis system designed to advance your whole genome association, linkage, and eQTL studies. Designed for biologists, statistical geneticists, and investigators responsible for generating genotyping data, the Syllego system provides you with an easy-to-use project workspace so that you can organize, analyze, and share your genotype and phenotype data along with your analysis results. With the Syllego system, generating high quality analysis data and meaningful results becomes simple. The Syllego system automates all tedious data management and data formatting tasks so that you can streamline your genetic analysis workflows using your analysis methods of choice. Managing all your genetic data and reference information is straightforward. The Syllego system converts public and private genotype data sets and reference annotations, such as dbSNP and HapMap, as well as individual (sample) information into a single, consistent repository for fast, convenient access.
- authors:
- web/ftp: http://www.rosettabio.com/products/syllego/
- source code language:
- operating systems:
- executables:
- reference:
- full name: Robust Transmission/Disequilibrium Test
- version: 1.0
- descriptions:
- authors:
- web/ftp: http://bios.ugr.es/~mabad/rTDT/index.html
- source code language: Matlab, C++
- operating systems:
- executables:
- reference: Sebastiani, Abad, Alpargu, Ramoni (2004), "Robust Transmission/Disequilibrium Test for incomplete family genotypes", Genetics, 168:2329-2337.
- full name:
- version: 1.2-6 (September 2010)
- descriptions: ADEGENET is a package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis.
- authors: Thibaut Jombart (email: jombart@biomserv.univ-lyon1.fr)
- web/ftp:
http://adegenet.r-forge.r-project.org/
http://cran.r-project.org/web/packages/adegenet/index.html - source code language: R
- operating systems:
- executables:
- reference: Jombart (2008), "adegenet: a R package for the multivariate analysis of genetic markers", Bioinformatics, 24:1403-1405.
- full name:
- version: 0.08 (August, 2010)
- descriptions: an R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data.
- authors: Řivind Skare (email: oivind.skare@medisin.uio.no
- web/ftp: http://folk.uio.no/thoree/FEST/
- source code language: R
- operating systems:
- executables:
- reference: Skare, Sheehan, Egeland (2009), "Identification of distant family relationships", Bioinformatics, 25(18):2376-2382.
- full name: R/Genetic Analysis Package
- version: 1.17-39 (July 2010)
- descriptions: This is an integrated package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates
- authors: Jinghua Zhao (MRC Epidemiology Unit at Strangeways Research Lab, UK) (email: jinghua.zhao@mrc-epid.cam.ac.uk ) in collaboration with other colleagues, and with help from Kurt Hornik of the R core
- web/ftp: http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm
- source code language: R
- operating systems:
- executables: aldh2, apoeapoc, bt, chow.test, fbsize, fsnps, gc.em, gcontrol, genecounting, gif, hap, hap.em, hap.score, hla, htr, hwe, hwe.hardy, kbyl, kin.morgan, makeped, mia, mtdt, muvar, pbsize, pfc, pgc, s2k, tbyt, whscore
- reference:
Zhao and Tan (2006),
"Integrated analysis of genetic data with R",
Human Genomics, 2(4):258-265.
reference manual (PDF): http://cran.r-project.org/doc/packages/gap.pdf
- full name:
- version: 1.6-4 (August 2010)
- descriptions:
GenABEL is a software created to facilitate whole-genome association analysis.
Specific features of GenABEL include:
* A range of functions specifically designed to help GWA analysis in samples of individuals from genetically isolated populations, and/or samples of related individuals (family-based design), and other analysis in presence of stratification
* Special functions oriented to meta-analysis
* Extensive documentation (about 100 pages of reference manual and 150 pages of tutorial)
* Many example data sets and exercises- authors:
- web/ftp: http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/
http://cran.r-project.org/web/packages/GenABEL/index.html- source code language: R
- operating systems:
- executables:
- reference: Aulchenko, Ripke, Isaacs, van Duijn (2007), "GenABEL: an R library for genome-wide association analysis", Bioinformatics, 23(10):1294-1296.
- full name:
- version: 1.2-4 (July 2010)
- 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
http://cran.r-project.org/web/packages/hapassoc/index.html - source code language: R
- operating systems:
- executables:
- reference:
- full name:
- version: 0.2-9 (August 2010)
- descriptions: plots measures of pairwise linkage disequilibria for SNPs
- authors: Ji-Hyung Shin (email: shin@sfu.ca), Sigal Blay, Nicholas Lewin-Koh, Brad McNeney, Jinko Graham
- web/ftp:
http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap
http://cran.r-project.org/web/packages/LDheatmap/index.html - source code language: R
- operating systems:
- executables:
- reference: Shin, Blay, McNeney, Graham (2006), "LDheatmap: an R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms", Journal of Statistical Software, 16, code snippet 3.
- full name: Likelihood Under Covariate Assumptions
- version:
- descriptions:
- authors: Ji-Hyung Shin (email: shin@sfu.ca), Brad McNeney, Jinko Graham
- web/ftp:
http://stat-db.stat.sfu.ca:8080/statgen/research/luca/
http://cran.r-project.org/web/packages/luca/index.html - source code language:
- operating systems:
- executables:
- reference: Shin, McNeney, Graham (2007), "Case-control inference of interaction between genetic and nongenetic risk factors under assumptions on their distribution", Statistical Applications in Genetics and Molecular Biology, 6(1):13.
- full name:
- version: 1.6 (June 2010)
- descriptions: Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.
- authors: Guido Schwarzer (email: sc@imbi.uni-freiburg.de)
- web/ftp: http://cran.r-project.org/web/packages/meta/index.html
- source code language: R
- operating systems:
- executables:
- reference:
- full name: METApopulation SIMulation
- version: 1.01
- descriptions: an R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop "null" distributions under various demographies.
- authors: Allan Strand (email: stranda@cofc.edu)
- web/ftp: http://linum.cofc.edu/software.html
- source code language: R, C++
- operating systems: UNIX, MS-Windows, MacOS
- executables:
- reference: A Strand (2002), "Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics", Mol Ecol Notes, 2:373-376.
- full name:
- version: 1.0-1 (April 2009)
- descriptions: ONEMAP is an environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants.
- authors: Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza, Antonio Augusto Franco Garcia (email: aafgarci@esalq.usp.br)
- web/ftp:
http://www.ciagri.usp.br/~aafgarci/OneMap/
http://cran.r-project.org/web/packages/onemap/index.html - source code language: R
- operating systems:
- executables: load.onemap, read.outcross, extract.group, remove.marker, arbitr.rf.2pts, est.rf.2pts, modigy.rf.2pts, group, map, make.map, est.rf.3pts
- reference: Garcia, Kido, Meza, Souza, Pinto, Pastina, Leite, Silva, Ulian, Figueira, Souza (2006), "Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases", Theoretical and Applied Genetics, 112:298-314.
- full name:
- version: 1.05-2 (November 2006)
- descriptions: Program for mapping quantitative trait loci in experimental crosses.
- Authors: Karl W. Broman (Johns Hopkins Univ, kbroman@jhsph.edu) and Hao Wu (The Jackson Laboratory)
- web/ftp: http://www.rqtl.org
- source code language: C and R
- operating systems: UNIX, MS-Windows, MacOS
- executables:
- reference: Broman, Wu, Sen, Churchill (2003), Bioinformatics, 19:889-890. [Medline]
- full name:
- version: 1.7.7 (April 2008)
- descriptions: QTLBIM, a library for QTL Bayesian Interval Mapping, provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits.
- authors:
- web/ftp: http://www.qtlbim.org/
- source code language: R
- operating systems:
- executables:
- reference:
- full name:
- version: v0.91 (May 2007)
- descriptions: R/qtlDesign is software to help plan quantitative trait locus (QTL) experiments.
- authors: Saunak Sen, Jaya Satagopan, Karl Broman, Gary Churchill
- web/ftp: http://www.epibiostat.ucsf.edu/biostat/sen/qtldesign-software/
- source code language: R
- operating systems:
- executables:
- reference:
- full name:
- version: 0.3 (October 2009)
- descriptions: snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files.
- authors: Augustin Luna, Kristin Nicodemus (email: augustin@mail.nih.gov)
- web/ftp:
http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html
http://cran.r-project.org/web/packages/snp.plotter/index.html - source code language: R
- operating systems:
- executables:
- reference: Luna, Nicodemus (2007), "snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package", Bioinformatics, 23(6):774-776.
- full name: SPECTRAL graph approach for GEnetic Matching
- version: 1 (July 2009)
- descriptions:
- authors: Ann Lee, Diana Luca, Lambertus Klei, Bernie Devlin, Kathryn Roeder
- web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/
- source code language: R
- operating systems:
- executables:
- reference: Lee, Luca, Klei, Devlin, Roeder (2010), "Discovering genetic ancestry using spectral graph theory", Genetic Epidemiology, 34(1):51-59.
- full name:
- version: 0.2-4 (November 2008)
- descriptions: A stepwise approach to identifying recombination breakpoints in a sequence alignment
- authors: Jinko Graham, Brad McNeney, Francoise Seillier-Moiseiwitsch, Sigal Blay
- web/ftp:
http://stat-db.stat.sfu.ca:8080/statgen/research/stepwise/
http://cran.r-project.org/web/packages/stepwise/index.html - source code language:
- operating systems:
- executables:
- reference:
- full name:
- version: 1.1-2 (November 2007)
- descriptions: a package for TDT with extended haplotypes in the "R" language. "R" is the public domain dialect of "S". It should be possible to port this library to the commercial "Splus" product. The main problem would be translation of the help files.
- Authors: David Clayton (Cambridge Institute, david.clayton@cimr.cam.ac.uk
- web/ftp:
http://www-gene.cimr.cam.ac.uk/clayton/software/
http://cran.r-project.org/web/packages/tdthap/index.html - source code language: R/Splus
- operating systems:
- executables:
- reference: Clayton, Jones (1999), "Transmission/disequilibrium tests for extended marker haplotypes", American Journal of Human Genetics, 65(4):1161-1169. [ abstract]
- full name: Rare Variants TESTS
- version:
- descriptions:
- authors: X Zhan, Youna Hu, G Abecasis (Univ Michigan)
- web/ftp: http://genome.sph.umich.edu/wiki/RvTests
- source code language: C++
- operating systems:
- executables:
- reference:
Province, Rice, Borecki, Gu, Kraja, Rao (2003),
"Multivariate and multilocus variance components method, based on
structural relationships to assess quantitative trait linkage via SEGPATH",
Genetic Epidemiology, 24(2):128-138.
http://www.stats.ox.ac.uk/~spencer/SelSim/Controlfile.html
The program sequenceLDhot is a method for detecting recombination
hotspots from population genetic data. It takes as input phased
(i.e. haplotype) data, together with an estimate of the
background recombination rate within the region (this is
allowed to vary across the region). Then sequenceLDhot considers
a grid of putative hotspot positions, and for each putative
hotspot calculates a likelihood ratio statistics for the presence
of a hotspot.
Fearnhead (2006),
"SequenceLDhot: detecting recombination hotspots",
Bioinformatics, 22:3061-3066.
ER Hauser, M Boehnke M (1998),
Biometrics, 54:1238-1246.
http://sift.jcvi.org/
http://blocks.fhcrc.org/sift/SIFT.html
Ng, Henikoff (2002),
"Accounting for human polymorphisms predicted to affect protein function",
Genome Research, 12:436-446.
Ng, Henikoff (2003),
"SIFT: Predicting amino acid changes that affect protein function",
Nucleic Acids Research, 31:3812-3814.
Kumar, Henikoff, Ng (2009),
"Predicting the effects of coding non-synonymous variants on protein
function using the SIFT algorithm",
Nature Protocols, 4:1073-1081.
http://watson.hgen.pitt.edu/register
online README file
MP Bass, ER Martin, ER Hauser (2004),
"Pedigree generation for analysis of genetic linkage and association",
Proceedings of the Pacific Symposium on Biocomputing, pp.93-103.
Ploughman, Boehnke (1989),
"Estimating the power of a proposed linkage study for a complex genetic trait",
American Journal of Human Genetics, 44(4):543-551.
[ abstract]
online documentation (version 4.1, april 1990)
Z Skrivanek, S Lin, ME Irwin (2003), "Linkage Analysis with Sequential Imputation",
Genetic Epidemiology, 25:25-35.
S Lin, Z Skrivanek, M Irwin (2003),
"Haplotyping using SIMPLE - caution on ignoring interference",
Genetic Epidemiology, 25:384-387.
The SIMLA3.3 with Graphical User Interface (GUI) is designed for users to set
up the SIMLA parameters conveniently. The GUI assists in creating a SIMLA control
file based on the parameters specified on the GUI panels. It includes the
SIMLA 3.2 program version.
http://wwwchg.duhs.duke.edu/research/simla3_3gui.html
http://simupop.sourceforge.net/
registration page at:
http://www.genetics.ucla.edu/software/registration
or,
http://watson.hgen.pitt.edu/register/
Sobel, Lange, O'Connell, Weeks (1996), in
Genetic Mapping and DNA Sequencing ,
Vol 81 in The IMA Volumes in Mathematics and its Applications,
eds TP Speed, MS Waterman (Springer-Verlag), pages 49-63.
Sobel, Lange (1996),
"Descent graphs in pedigree analysis: applications to
haplotyping, location scores, and marker sharing statistics",
American Journal of Human Genetics, 58(6):1323-1337.
[ abstract]
Sobel, Sengul, Weeks (2001),
Human Heredity, 52:121-131.
Sobel, Papp, Lange (2002),
"Detection and integration of genotyping errors in
statistical genetics",
American Journal of Human Genetics, 70(2):496-508.
[ html]
SIMWALK manual
FAQ-O-MATIC:
http://watson.hgen.pitt.edu/fom-serve/cache/20.html
Wu, Kraft, Epstein, Taylor, Chanock, Hunter, Lin (2010),
"Powerful SNP set analysis for case-control genomeWide association studies",
American Journal of Human Genetics , 86:929-942.
Weeks, Ott, Lathrop (1990),
American Journal of Human Genetics, 47(suppl):A204.
online documentation
FAQ-O-MATIC:
http://watson.hgen.pitt.edu/fom-serve/cache/20.html
Van Os, Stam, Visser, Van Eck (2005),
"RECORD: A novel method for ordering loci on a genetic linkage map",
Theoretical and Applied Genetics, 112(1):30-40.
[abstract]
Van Os, Andrzejewski, Bakker, Barrena, Bryan, Caromel, Ghareeb, Isidore,
de Jong, van Koert, Lefebvre, Milbourne, Ritter, van der Voort, Rousselle-Bourgeois,
van Vliet, Waugh, Visse, Bakke, Van Eck (2006),
"Construction of a 10,000-marker ultradense genetic recombination
map of potato: Providing a framework for accelerated gene isolation and
a genomewide physical map",
Genetics, 173(2):1075-1087.
[abstract]
http://soap.genomics.org.cn/soap3.html (SOAP3)
http://soap.genomics.org.cn/soapsnp.html (SOAP SNP)
http://soap.genomics.org.cn/soapindel.html (SOAP indel)
http://soap.genomics.org.cn/SOAPsv.html (SOAP structural variants)
Li, Li, Fang, et al. (2009),
"SNP detection for massively parallel whole-genome resequencing",
Genome Research, 19:1124-1132.
Li, Yu, Li, Lam, Yiu, Kristiansen, Wang (2009),
"SOAP2: an improved ultrafast tool for short read alignment",
Bioinformatics, 25(15):1966-1967.
Almasy, Blangero (1998),
"Multipoint quantitative-trait linkage analysis in general pedigrees",
American Journal of Human Genetics, 62(5):1198-1211 (1998)
[ abstract]
http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434
Holmans and Clayton (1995), submitted.
online manual
Gordon, Haynes, Johnnidis, Patel, Bowcock, Ott (2004),
"A transmission disequilibrium test for general pedigrees
that is robust to the presence of random genotyping errors
and any number of untyped parents",
European Journal of Human Genetics, 12:752-761.
User's Guide
http://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware.aspx?Software_Id=20
ftp://odin.mdacc.tmc.edu/pub/source/tdtasp_1.1.tar.gz (source)
ftp://odin.mdacc.tmc.edu/pub/sun/tdtasp_1.0.tar.gz (Solaris Executable)
ftp://odin.mdacc.tmc.edu/pub/win32/tdtasp_1.1_se.exe (Windows executable)
http://www.biostat.jhsph.edu/~wmchen/pc.html
Spielman, Ewens (1998),
"A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test",
American Journal of Human Genetics, 62(2):450-458.
[ abstract]
Schork, Boehnke, Terwilliger, Ott (1993),
"Two-trait-locus linkage analysis: a powerful strategy for mapping complex genetic traits",
American Journal of Human Genetics, 53(5):1127-1136.
[ abstract]
online documentation
ftp://ftp.nhgri.nih.gov/pub/software/TRAP/
Sorant, Cai, Sung, Kim, Wilson (2010), "Tiled Regression Analysis
Package (TRAP): software implementation of tiled regression methodology",
Abstract 244. In: "Abstracts from the nineteenth annual meeting of the International
Genetic Epidemiology Society",
Genetic Epidemiology, 34:984-985.
Zollner, Wen, Pritchard (2005),
"Association mapping and fine mapping with TreeLD",
Bioinformatics, 21(14):3168-3170.