- 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.
- 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), American Journal of Human Genetics, 66:279-292.
- 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.
- 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:
WJ Gauderman (2002), "Sample size requirements for matched case-control studies of
gene-environment interaction", Stat Med 21:35-50.
WJ Gauderman (2002), "Sample size requirements for association studies of gene-gene interaction", American Journal of Epidemiology, 155:478-484.
WJ Gauderman (2003), "Candidate gene association studies for a quantitative trait, using parent-offspring trios", Genetic Epidemiology, 25:327-338.
- 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
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:
M Knapp (1999), "The transmission/disequilibrium test and parental-genotype
reconstruction: the reconstruction-combined transmission/disequilibrium test",
American Journal of Human Genetics, 64:861-870.
M Knapp (1999b), "Using exact P values to compare the power between the reconstruction-combined transmission/disequilibrium test and the sib transmission/disequilibrium test", American Journal of Human Genetics, 65:1208-1210.
S Horvath, NM Laird, M Knapp (2000), "The transmission/disequilibrium test and parental-genotype reconstruction for X-chromosomal markers", American Journal of Human Genetics, 66:1161-1167.
- 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.
- RELATIVE
- 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, "Relationship estimation in affected sib pair analysis of late-onset diseases", Eur J Hum Genet 5, 69-77 (1997).
- RELCHECK
- 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),
American Journal of Human Genetics, 61:423-429.
[Medline]
Broman, Weber (1998), American Journal of Human Genetics, 63:1563-1564. [Medline]
- RELPAIR
- 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)).
- RELTYPE
- 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)).
- R/GAP
- full name: R/Genetic Analysis Package
- version: 1.0.8 (April 2006)
- 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
- RHMAP
- 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),
American Journal of Human Genetics, 49:1174-1188.
Lange,Boehnke, Cox, Lunetta, Genome Research, 5,136-150 (1995).
Lunetta,Boehnke, Lange, Cox, Genome Research, 5, 151-163 (1995).
- RHMAPPER
- 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. Science, 270, 1945-1954 (1995).
Slonim, Stein, Kruglyak, Lander, in preparation (1996).
online user's guide
- RISCALW
- 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.
- R/METASIM
- 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.
- ROSATTA SYLLEGO SYSTEM
- 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:
- R/QTL
- 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]
- RTDT
- 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.
S - SAGE
- full name:Statistical Analysis for Genetic Epidemiology
- version: 5.3
- descriptions: The S.A.G.E. software provides researchers with the tools necessary for various types of statistical genetic analysis of human family data.
- authors: R. Elston, J. Bailey-Wilson, G. Bonney, L. Tran, B. Keats, A. Wilson
- web/ftp: http://darwin.cwru.edu/sage/
- source code language: C [version 4.0 will be in C++]
- operating systems: UNIX(DEC UNIX/Solaris), MS-Windows (95/NT), Linux
- executables: assoc, fcor, freq, genibd, lodlink, lodpal, markerinfo, mlod, pedinfo, reltest, segreg, sibpal, tdtex
- reference:
- SASGENE
- full name:
- version: 1.2 (March 1999)
- descriptions: a SAS computer program for gene segregation and linkage analysis in breeding population
- authors: Jinsheng Liu, Todd Wehner, Sandy Donaghy
- web/ftp: http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html
- source code language: SAS
- operating systems:
- executables:
- reference: Liu, Wehner, Donaghy (1997), "SASGENE: A SAS computer program for genetic analysis of gene segregation and linkage", Journal of Heredity, 88:253-254.
- SAS/GENETICS
- full name:
- version: add-on to the SAS System, Release 8.2
- descriptions: Software for summarizing marker properties (allele & genotype frequencies, tests for Hardy-Weinberg equilibrium, measures of marker informativeness), examining marker-marker relationships (tests and measures of linkage disequilibrium, and haplotype frequency estimation), and exploring marker-trait associations using case-control or family-based tests
- Authors: W Czika, X Yu
- web/ftp:
- source code language: C
- operating systems: MS-Windows, UNIX(HPUX/AIXR/Solaris/..), MVS
- executables:
- reference: introduction
- price: please contact shannon.conners@jmp.com for details
- SASQUANT
- full name:
- version: 1.1 (May 2005)
- descriptions: a SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations
- authors: Gabriele Gusmini, Todd Wehner , Sandy B. Donaghy
- web/ftp: http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html
- source code language: SAS
- operating systems:
- executables:
- reference: Gusmini, Wehner, Donaghy (2005), "SASQuant: A SAS software program to estimate genetic effects and heritabilities of quantitative traits in populations consisting of six related generations", Journal of Heredity, to appear.
- SCOUT
- full name:
- version: beta-0.9.3
- descriptions: Scout is a software program for conducting combined association analysis of triads and unrelated subjects
- authors: Richard Duncan and Michael Epstein (Emory University, email: statgen@genetics.emory.edu)
- web/ftp: http://www.genetics.emory.edu/labs/epstein/software/scout/index.html
- source code language: Fortran (CVF 6.6) with IMSL routines
- operating systems: MS-Windows(2000/XP)
- executables: scout_cl.exe, scout_gui.exe
- reference: Epstein, Veal, Trembath, Barker, Li, Satten (2005), "Genetic association analysis using data from triads and unrelated subjects", American Journal of Human Genetics, 76:592-608.
- SDMINP
- full name: Step-Down MIN P-value
- version: 1.0 (December 2005)
- descriptions: SDMinP is an easy-to-use program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics.
- authors: Markus Obreiter, Lars Beckmann (email: l.beckmann@dkfz.de)
- web/ftp: http://www.dkfz.de/SDMinP/
- source code language: Python 2.3.5
- operating systems: UNIX, Linux, MS-Windows
- executables:
- reference: Obreiter, Fischer, Chang-Claude, Beckmann (2005), "SDMinP: a program to control the family wise error rate using step-down minP adjusted p-values", Bioinformatics, 21(14):3183-3184.
- SEGPATH
- full name: SEGregation analysis and PATH analysis
- version:
- descriptions:
- authors: Michael A. Province (email: mike@wubios.wustl.edu)
- web/ftp: http://www.biostat.wustl.edu/~mike/segpath/
- source code language:
- operating systems:
- executables:
- reference:
Province, Rao (1995),
"General purpose model and a computer program for combined segregation
and path analysis (SEGPATH): automatically creating computer programs
from symbolic language model specifications",
Genetic Epidemiology, 12(2):203-219.
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.
- SELSIM
- full name:
- version: 2.1 (June 2005)
- descriptions: When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. SELSIM is a program which can simulate population genetic data in which a single site has experienced natural selection.
- authors: Chris Spencer (Univ of Oxford, email: spencer@stats.ox.ac.uk)
- web/ftp:
http://www.stats.ox.ac.uk/mathgen/software.html
http://www.stats.ox.ac.uk/~spencer/SelSim/Controlfile.html - source code language: C,C++
- operating systems: MS-Windows(XP), Linux
- executables:
- reference: Spencer, Coop (2004), "SelSim: a program to simulate population genetic data with natural selection and recombination", Bioinformatics, 20:3673-3675.
- SGS
- full name:
- version: 1.0d
- descriptions:
- authors: Bernd Degen
- web/ftp: http://software.bfh-inst2.de/download3.html
- source code language: VisualBasic
- operating systems: MS-Windows (95/98/00/NT)
- executables:
- reference: Degen, Petit, Kremer (2001), "SGS - Spatial Genetic Software: a computer program for analysis of spatial genetic and phenotypic structures of individuals and populations", Journal of Heredity, 92(5):447-448.
- SIBERROR
- full name: SibError
- version: 1.0 (November 20, 1997)
- descriptions: SibError is an algorithm that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers.
- Authors: Drs. Meg Gelder Ehm (mge37216@glaxowellcome.com) and Michael Wagner ( mw29911@glaxowellcome.com) (Glaxo Wellcome, Inc.)
- web/ftp:
- source code language: C
- operating systems: UNIX
- executables: siberror
- reference: Ehm, Wagner, "Test statistic to detect errors in sib-pair relationship", American Journal of Human Genetics, (Jan 1998)
- SIBLINK
- full name:
- version: 3.0
- descriptions: SIBLINK allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors.
- authors: Elizabeth Hauser, Mike Boehnke, William Duren
- web/ftp: http://wwwchg.duhs.duke.edu/software/siblink.html
- source code language: C++
- operating systems: UNIX(Solaris), Linux
- executables: siblink3.0
- reference:
ER Hauser, M Boehnke, SW Guo, N Risch (1996),
Genetics Epidemiology. 13:117-137.
ER Hauser, M Boehnke M (1998), Biometrics, 54:1238-1246.
- SIBMED
- full name: SIBling Mutation and Error Detection
- version: 1.0
- descriptions: SIBMED identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping.
- Authors: Julie A Douglas, Michael Boehnke (Univ Michigan)
- web/ftp: http://csg.sph.umich.edu/boehnke/sibmed.php
- source code language: FORTRAN 77
- operating systems: MS-Windows, UNIX
- executables: sibmed.exe
- reference: JA Douglas, M Boehnke, K Lange (2000), American Journal of Human Genetics, 66:1287-1297.
- SIB-PAIR
- full name:
- version: 1.00a (January 2007)
- descriptions: Program SIB-PAIR performs a number of simple analyses of family data that tend to be "nonparametric" or "robust" in nature, includes IBD and IBS based APM, Haseman-Elston sib pair, TDT and association analyses.
- Authors: David Duffy (Queensland Institute of Med Res, Australia, davidd@qimr.edu.au )
- web/ftp: http://www2.qimr.edu.au/davidD
- source code language: Fortran77
- operating systems:
- executables:
- reference: Am. Soc. Hum. Genet. Annual Meeting 1997 (Duffy, Am.J. Hum. Genet. suppl. 61, A197 (1997)); online manual page
- SIBSIM
- full name:
- version: 2.1.2 (November 2005)
- descriptions: Simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scalable way. It is based on XML, completely written in C++ and published under the GNU General Public License.
- authors: Daniel Franke (University Hospital Schleswig-Holstein)
- web/ftp: http://www.imbs.uni-luebeck.de/pub/sibsim/index.html
- source code language: C++, XML
- operating systems: UNIX
- executables:
- reference: D Franke, A Kleensang and A Ziegler (2006), "SIBSIM, quantitative phenotype simulation in extended pedigrees", GMS Med Inform Biom Epidemiol, 2(1):Doc04.
- SILCLOD
- full name: SIgnificance Levels and Critical LODs
- version:
- descriptions: calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified.
- authors: Andreas Ziegler (email: koenigir@imbs.uni-luebeck.de)
- web/ftp: http://www.imbs.uni-luebeck.de/pub/silcLOD/index.html
- source code language:
- operating systems:
- executables:
- reference: E Lander, L Kruglyak (1995), "Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results", Nature Genetics, 11:241-247.
- SIMCOAL
- full name: SIMulate COAlescence
- version: 1.0
- descriptions:
- authors: Laurent Excoffier (email: laurent.excoffier@zoo.unibe.ch)
- web/ftp: http://cmpg.unibe.ch/software/simcoal/
- source code language: C++
- operating systems: MS-Windows(9X/NT)
- executables: simcoal, sim_coal
- reference: Excoffier, Novembre, Schneider (2000), "SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography", Journal of Heredity, 91:506-509.
- SIMHAP
- full name: SIMulation-based HAPlotypic analysis
- version: Beta 2.1 (March 2006)
- descriptions: SimHap uses biallelic SNP genotype data to impute haplotype frequencies at the individual level. SimHap also tests for haplotype associations with outcomes of interest while incorporating the uncertainty around inferred haplotypes into the modelling procedure. SimHap allows epidemiological (ie, non-genetic) and both single SNP and haplotype association analyses of quantitative Normal, binary, longitudinal and right-censored outcomes under a range of genetic models. SimHap can accommodate large data sets, and can model genetic and environmental effects, including complex haplotype:environment interactions. SimHap features cross-platform functionality via Java, and a sophisticated graphical user interface (GUI). SimHap will also perform association analysis on more simple epidemiological models, with or without the inclusion of genetic covariates.
- authors: Pamela A. McCaskie (Univ. of Western Australia), Kim W Carter, Lyle J Palmer
- web/ftp: http://www.genepi.org.au/simhap
- source code language: Java (1.5)
- operating systems: web-based
- executables:
- reference:
- SIMIBD
- full name:
- version: 1.21 (Jan 1997)
- descriptions:
- authors: Sean Davis ( davis@moriarty.hgen.pitt.edu ) and Daniel E. Weeks
- web/ftp:
http://watson.hgen.pitt.edu/register/soft_doc.html,
http://watson.hgen.pitt.edu/~davis/
http://watson.hgen.pitt.edu/register - source code language: C
- operating systems: UNIX(SunOS/Solaris/HP/DEC-UNIX)
- executables: simibd, xslink
- reference:
Davis, Schroeder, Goldin, Weeks (1996),
American Journal of Human Genetics, 58:867-880.
online README file
- SIMLA
- full name: SIMulation of pedigree data for Linkage and Association studies
- version: 2.3 (Oct 2003)
- descriptions: SIMLA is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages
- authors: Elizabeth Hauser, Eden Martin, Meredyth Bass
- web/ftp: http://wwwchg.duhs.duke.edu/software/simla.html
- source code language: C++
- operating systems: UNIX(Solaris), Linux
- executables: simla2.3
- reference:
MP Bass, ER Martin, ER Hauser(2002), Am J Hum Genet, suppl 71:569.
MP Bass, ER Martin, ER Hauser(2004), Proceedings of the Pacific Symposium on Biocomputing, in press.
- SIMLINK
- full name:
- version: 4.12 (April 1997)
- descriptions: a computer program to estimate the probability ("power") of detecting linkage given family history information on a set of identified pedigrees.
- authors: Michael Boehnke ( boehnke@sph.umich.edu)
- web/ftp: http://csg.sph.umich.edu/boehnke/simlink.php
- source code language: FORTRAN
- operating systems: MS-DOS, UNIX(SunOS/..), VMS
- executables:
- reference:
Boehnke,
American Journal of Human Genetics, 39, 513-527 (1986).
Ploughman, Boehnke, American Journal of Human Genetics, 44, 543-551 (1989).
online documentation (version 4.1, april 1990)
- SIMPED
- full name:
- version:
- descriptions: SimPed is a program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.
- authors: SM Leal, K Yan, B Müller-Myhsok
- web/ftp: http://www.hgsc.bcm.tmc.edu/genemapping
- source code language: C
- operating systems: UNIX, MS-Window, Linux
- executables:
- reference: Leal, Yan, Muller-Myhsok (2005), "SimPed: a simulation program to generate haplotype and genotype data for pedigree structures", Human Heredity, 60(2):119-122.
- SIMPLE
- full name: Sequential Imputation for MultiPoint Linkage Estimation
- version:
- descriptions: Calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation.
- authors: S Lin, Z Skrivanek, M Irwin (Ohio State Univ)
- web/ftp: http://www.stat.ohio-state.edu/~statgen/SOFTWARE/SIMPLE/
- source code language: C
- operating systems: UNIX(Solaris)
- executables: simple, scan
- reference:
M Irwin, N Cox, A Kong (1994),
"Sequential imputation for multilocus linkage analysis",
Proceddings of the National Academy of Sciences , 91:1684-1688
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.
- SIMULATE
- full name:
- version:
- descriptions: a program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package.
- authors: Joe Terwilliger (Columbia University), Jurg Ott (Rockefeller University)
- web/ftp: ftp://linkage.rockefeller.edu/software/simulate
- source code language: Pascal
- operating systems: MS-DOS, VMS, UNIX
- executables:
- reference: online documentation
- SIMUPOP
- full name:
- version: 0.6.0 (Jan 2005)
- descriptions: simuPOP is a forward-based population genetics simulation program. It is capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it.
- authors: Bo Peng (email:bpeng@rice.edu)
- web/ftp:
http://bp6.stat.rice.edu:8080/simuPOP/
http://simupop.sourceforge.net/ - source code language: C++ (provided as Python libraries)
- operating systems:
- executables:
- reference: Peng, Kimmel (2005), "simuPOP: a forward-time population genetics simulation environment", Bioinformatics, 21(18):3686-3687.
- SIMWALK
- full name:
- alias: SIMWALK/SIMCROSS
- version: SIMCROSS: June 1995; SIMWALK2: 2.91 (December 2004)
- descriptions: programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method.
- authors: Eric Sobel (UCLA. email: simwalk@genetics.ucla.edu (in collaboration with Kenneth Lange, Jeffrey O'Connell, and Daniel E. Weeks)
- web/ftp:
http://www.genetics.ucla.edu/software/simwalk
registration page at: http://www.genetics.ucla.edu/software/registration or, http://watson.hgen.pitt.edu/register/ - source code language: FORTRAN77
- operating systems: UNIX(SunOS/Solaris)
- executables:
- reference:
Weeks, Sobel, O'Connell, Lange,
American Journal of Human Genetics, 56, 1506-1507 (1995).
Sobel, Lange, O'Connell, Weeks, in Genetic Mapping and DNA Sequencing , Vol 81 in The IMA Volumes in Mathematics and its Applications, eds TP Speed, MS Waterman (Springer-Verlag, 1996), 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, 58:1323-1337.
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, 70:496-508.
SIMWALK manual
FAQ-O-MATIC: http://watson.hgen.pitt.edu/fom-serve/cache/20.html
- SLINK (see also FASTSLINK )
- full name:
- version:
- descriptions:
- authors: Daniel E. Weeks, Jurg Ott
- web/ftp: ftp://linkage.rockefeller.edu/software/slink
- source code language: Pascal
- operating systems: MS-DOS
- executables: slink, isim, lsim, msim
- reference:
Ott (1989),
Proceddings of the National Academy of Sciences , 86:4175-4178.
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
- SNAP
- full name: Suite of Nucleotide Analysis Programs
- version:
- descriptions: The exploration of DNA sequence variation for making inferences on evolutionary processes in populations requires the coordinated implementation of a Suite of Nucleotide Analysis Programs (SNAP), each bound by specific assumptions and limitations. We have developed a workbench tool to make existing population genetic software more accessible and to facilitate the integration of new tools for analyzing patterns of DNA sequence variation, within a phylogenetic context. Collectively, SNAP tools can serve as a bridge between theoretical and applied population genetic analysis.
- authors: David Aylor, Eric Price, Ignazio Carbone (North Carolina State Univ)
- web/ftp: http://www.cals.ncsu.edu/plantpath/people/faculty/carbone/snap.html
- source code language:
- operating systems:
- executables:
- reference: Aylor, Price, Carbone (2006), "SNAP: Combine and Map modules for multilocus population genetic analysis", Bioinformatics, 22(11):1399-1401.
- SNPALYZE
- full name:
- version: 6.0 (December 2006)
- descriptions:
- authors: dynacom.co.jp
- web/ftp: http://www.dynacom.co.jp/e/products/package/snpalyze/index.html
- source code language:
- operating systems: MS-Windows (98/Me/NT4.0/2000/XP)
- executables:
- reference: Shimo-Onoda, Tanaka, Furushima, Nakajima, Toh, Harata, Yone, Komiya, Adachi, Nakamura, Fujimiya, Inoue(2002), "Akaike's information criterion for a measure of linkage disequilibrium", J Hum Genet, 47(12): 649-655.
- SNP ASSISTANT
- full name:
- version: 1.0.11 (April 2004)
- descriptions: SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects.
- authors: Biodata Ltd., Estonia (snpassistant@biodata.ee)
- web/ftp: http://www.biodata.ee/SNPassistant.htm (30 days trial version)
- source code language: C++
- operating systems: MS-Windows(95 and newer)
- executables:
- reference: online manual: http://www.biodata.ee/sa/SNP_Assistant_Manual_1.0.7.pdf
- SNP CHART
- full name:
- version:
- descriptions: The purpose of this software is to generate visual patterns that can be easily interpreted as a single specific Single Nucleotide Polymorphism (SNP) genotype, based on reiterative pattern recognition from validated SNP data
- authors: Scott Tebbutt (email: stebbutt@mrl.ubc.ca)
- web/ftp: http://www.snpchart.ca/
- source code language: Java
- operating systems: web-based
- executables:
- reference: Tebbutt, Opushnyev, Tripp, Kassamali, Alexander, Andersen (2005), "SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data", Bioinformatics, 21(1):124-127.
- SNPEM
- full name: SNP Expectation Maximization
- version:
- descriptions: EM algorithm estimations of SNP haplotypes
- authors:
- web/ftp: http://polymorphism.ucsd.edu/snpem/
- source code language:
- operating systems: web-based
- executables:
- reference:
- SNPHAP
- full name:
- version: 0.2 (Jan 2002)
- descriptions: a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects
- Authors: David Clayton (Cambridge Institute, david.clayton@cimr.cam.ac.uk
- web/ftp: http://www-gene.cimr.cam.ac.uk/clayton/software/
- source code language: C,C++
- operating systems:
- executables:
- reference:
- SNP-HWE
) and Goncalo Abecasis- full name:
- version:
- descriptions: a fast exact Hardy-Weinberg Equilibrium test for SNPs
- authors: Janis Wigginton (email: "a href="mailto:wiggie@umich.edu"> wiggie@umich.edu
- web/ftp: http://www.sph.umich.edu/csg/abecasis/Exact/index.html
- source code language: Fortran, C,C++, R
- operating systems:
- executables:
- reference: Wigginton, Cutler, Abecasis (2005), "A note on exact tests of Hardy-Weinberg equilibrium", American Journal of Human Genetics, 76(5):887-893.
- full name:
- version:
- descriptions: Multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available.
- authors: Emily Webb (The Institute for Cancer Research, email: emily.webb@icr.ac.uk)
- web/ftp: http://www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm
- source code language: Perl
- operating systems: UNIX
- executables:
- reference: Webb, Sellick, Houlston (2005), "SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal", Bioinformatics, 21:3060-3061.
- full name: Single Nucleotide Polymorphism Processor
- version: 1.0 (2003)
- descriptions: a dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.
- authors: Lanjuan Zhao ( lanjuanzhao@creighton.edu), Miaoxin Li ( limx54@163.com), Yanfang Guo, Fuhua, Xu, Jinlong Li and Hongwen Deng.
- web/ftp: http://orclinux.creighton.edu/snpp/
- source code language: Java
- operating systems: Windows, Linux, Solaris, MacOS
- executables:
- reference: Zhao, Li, Guo, Xu, Li, Deng (2005), "SNPP: automating large-scale SNP genotype data management", Bioinformatics, 21:266-268
- full name: SNP STATStics
- version:
- descriptions: SNPStats is a simple, ready-to-use software which has been designed to analyze genetic-epidemiology studies of association using SNPs.
- authors: Victor Moreno (email: v.moreno@ico.scs.es) Xavier Sole (email: x.sole@ico.scs.es)
- web/ftp: http://bioinfo.iconcologia.net/snpstats/
- source code language:
- operating systems: web-based
- executables:
- reference: Sole, Guino, Valls, Iniesta, Moreno (2006), "SNPStats: a web tool for the analysis of association studies", Bioinformatics, 22(15):1928-1929.
- full name: Sequential Oligogenic Linkage Analysis Routines
- version: 4.0.7 (December 2006).
- descriptions: OLAR is a flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis.
- Authors: John Blangero (john@darwin.sfbr.org), Kenneth Lange, Laura Almasy (almasy@darwin.sfbr.org), Tom Dyer (tdyer@darwin.sfbr.org), Charles Peterson (charlesp@darwin.sfbr.org).
- web/ftp: http://www.sfbr.org/solar/index.html
- source code language: FORTRAN, C, C++, TCL
- operating systems: UNIX(Solaris7-9/Solaris x86 8-9/Digital Unix 4.0e/SG Irix), Linux
- executables: solar, ibdprep, ibdmat, relate, multipnt
- reference:
Blangero, Almasy, "SOLAR: sequential oligogenic
linkage analysis routines", Population Genetics Laboratory
Technical Report No. 6, Southwest Foundation for Biomedical
Research, San Antonio, TX 78228 (1996);
Almasy, Blangero, "Multipoint quantitative-trait linkage analysis in general pedigrees", American Journal of Human Genetics, 62:1198-1211 (1998)
- full name: Statistics Program for Analysing Mixtures
- version: 3.7b
- descriptions: SPAM estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem.
- authors:
- web/ftp: http://www.genetics.cf.adfg.state.ak.us/software/spampage.php
- source code language:
- operating systems:
- executables:
- reference: Debevec, Gates, Masuda, Pella, Reynolds, Seeb (2000), "SPAM (version 3.2): statistics program for analyzing mixtures", Journal of Heredity, 91:509-511.
- full name:
- version:
- descriptions: analysis of sperm typing data.
- authors: Kenneth Lange (UCLA), Laura Lazzeroni
- web/ftp: registration page at: http://www.biomath.medsch.ucla.edu/faculty/klange/software.html
- source code language: FORTRAN77
- operating systems:
- executables:
- reference: Lazzeroni, Arnheim, Schmitt, Lange (1994), American Journal of Human Genetics, 55:431-436.
- full name:
- version:
- descriptions: analysis of segregation in single-sperm data
- Authors: MS McPeek ( mcpeek@galton.uchicago.eduUniv Chicago)
- web/ftp: http://galton.uchicago.edu/~mcpeek/software/spermseg
- source code language: C
- operating systems:
- executables:
- reference: MS McPeek, American Journal of Human Genetics, 65:1195-1197 (1999).
- full name: Simulate Pedigree In Population
- version:
- descriptions: Simulate pedigrees and genetic data in age-structured populations
- authors: Eric C Anderson, K.K. Dunham (Southwest Fisherie Science Center)
- web/ftp:
http://swfsc.noaa.gov/staff.aspx?id=740
http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434 - source code language: C
- operating systems:
- executables:
- reference: Anderson, Dunham (2005), "SPIP 1.0: a program for simulating pedigrees and genetic data in age-structured populations", Molecular Ecology Notes, 5(2):459-461.
- full name: Sib Pair Linkage Analysis Testing
- version: 1.0 (2006)
- descriptions: SPLAT can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility.
- authors: Katarzyna Adamska (email: adamska@elf.ii.uj.edu.pl), David Poznik (email: david.poznik@joslin.harvard.edu), Xin Xu (email: xin_xu@harvard.edu)
- web/ftp: http://www.joslinresearch.org/LabSites/Krolewski/splat/
- source code language: C++, Qt
- operating systems: UNIX(SunOS),Linux, MacOS, MS-Windows(2000/XP)
- executables:
- reference: Poznik, Adamska, Xu, Krolewski, Rogus (2006), "A novel framework for sib pair linkage analysis", American Journal of Human Genetics, 78:222-230.
- full name: affected Sib Pairs LINKage analysis
- version: 1.09 (Nov 1999)
- descriptions: linkage analysis using affected sib pairs
- authors: David Clayton (Cambridge Institute, david.clayton@cimr.cam.ac.uk
- web/ftp: http://www-gene.cimr.cam.ac.uk/clayton/software/
- source code language: c++
- operating systems: UNIX(SunOS/..), MS-DOS
- executables: splink, ped2spl
- reference:
Holmans (1993),
American Journal of Human Genetics, 52:362-374.
Holmans and Clayton, submitted (1995).
online manual
- full name:
- version:
- descriptions: semiparametric family-based association
- authors: Guoqing Diao (email: gdiao@gmu.edu), Danyu Lin
- web/ftp: http://www.bios.unc.edu/~lin/software/SQTDT/
- source code language:
- operating systems: Linux
- executables:
- reference: Diao, Lin (2006), "Improving the power of association tests for quantitative traits in family studies", Genetic Epidemiology, 30:301-313.
- full name: Semiparametric QTL mapping in general pedigrees
- version:
- descriptions:
- authors: Guoqing Diao (email: gdiao@gmu.edu), Danyu Lin
- web/ftp: http://www.bios.unc.edu/~lin/software/SQTL/
- source code language:
- operating systems: Linux
- executables:
- reference: Diao, Lin (2005), "A powerful and robust method for mapping quantitative trait loci in general pedigrees", American Journal of Human Genetics, 77:97-111.
- full name:
- version:
- descriptions: Finds starting points for MCMC analysis performed on large, complex pedigrees and polymorphic markers.
- authors: Y Luo, S Lin (Ohio State Univ)
- web/ftp: http://www.stat.ohio-state.edu/~statgen/SOFTWARE/START/
- source code language:
- operating systems: UNIX(Solaris), Linux
- executables:
- reference: Y Luo, S Lin (2003), "Finding starting points for Markov chain Monte Carlo analysis of genetic data from large and complex pedigrees", Genetic Epidemiology, 25:14-24.
- full name: STatistical Explanation for Positional Cloning
- version:
- descriptions:
- authors: Lei Sun, Nancy COx, Mary Sara McPeek
- web/ftp: http://hg-wen.uchicago.edu/software.html
- source code language:
- operating systems:
- executables:
- reference: Sun, Cox, McPeek (2002) "A statistical method for identification of polymorphisms that explain a linkage result", American Journal of Human Genetics, 70:399-411.
- full name:
- version: 1.1
- descriptions: a companion program to structure. This is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure.
- authors: Jonathan Pritchard (email: pritch@genetics.uchicago.edu )
- web/ftp: http://pritch.bsd.uchicago.edu/software/STRAT.html
- source code language:
- operating systems: MS-DOS, MS-Windows,UNIX(Solaris), Linux
- executables:
- reference: JK Pritchard, M Stephens, NA Rosenberg, P Donnelly (2000), "Association mapping in structured populations", American Journal of Human Genetics, 67:170-181.
- full name:
- version: 2.1 (August 2004)
- descriptions: using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs and SNPs.
- authors: Jonathan Pritchard (email: pritch@genetics.uchicago.edu )
- web/ftp: http://pritch.bsd.uchicago.edu/software.html
- source code language:
- operating systems: MS-DOS, MS-Windows, UNIX(Solaris), Linux
- executables:
- reference: JK Pritchard, M Stephens, P Donnelly (2000), "Inference of population structure using multilocus genotype data", Genetics 155: 945-959.
- full name: Slink Utility Program
- version: 060629
- descriptions: an extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with a trait locus.
- authors: Mathieu Lemire (email:mathieu.lemire@mail.mcgill.ca)
- web/ftp: http://www.genome.mcgill.ca/~mlemire
- source code language: C,C++
- operating systems: UNIX, LINUX, CYGWIN
- executables:
- reference: Lemire (2006), "SUP: An extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values", BMC Genetics, 7:40.
- full name:
- version: 1.6 (March 2006)
- descriptions: the program performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs.
- authors: Ma'ayan Fishelson (email: fmaayan@cs.technion.ac.il)
- web/ftp: http://bioinfo.cs.technion.ac.il/superlink/
- source code language:
- operating systems: UNIX, MS-Windows, Linux, MacOS X
- executables:
- reference: M Fishelson, D Geiger (2002), Bioinformatics, 18(suppl 1):S189-S198.
- full name: Semiparametric Variance-Component for Censored data
- version:
- descriptions:
- authors: Guoqing Diao (email: gdiao@gmu.edu), Danyu Lin
- web/ftp: http://www.bios.unc.edu/~lin/software/SVCC/
- source code language:
- operating systems: Linux
- executables:
- reference: Diao, Lin (2006), "Semiparametric variance-component models for linkage and association analyses of censored trait data", Genetic Epidemiology, 30:570-581.
Gordon, Haynes, Johnnidis, Patel, Bowcock, Ott
(2004), Eur. J. Hum. Geneti. in press.
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)
Schork, Boehnke, Terwilliger, Ott (1993),
American Journal of Human Genetics, 53,1127-1136.
online documentation
Zollner, Wen, Pritchard (2005),
"Association mapping and fine mapping with TreeLD",
Bioinformatics, 21(14):3168-3170.
ftp://mapper.wustl.edu/pub/two-d
Zapata, Carollo, Rodriguez (2001),
"Sampling variance and distribution of the D' measure
of overall gametic disequlibrium between multiallelic loci",
Annals of Human Genetics, 65:395-406.
online user's guide (Dec 1993)
online user's guide
(Dec 1993)
Rieder, Taylor, Clark, Nickerson (1999),
"Sequence variation in the human angiotensin converting enzyme",
Nature Genetics, 22:59-60.
Rieder, Taylor, Clark, Nickerson (1999),
"Sequence variation in the human angiotensin converting enzyme",
Nature Genetics, 22:59-60.
http://watson.hgen.pitt.edu/register
O'Connell,Weeks, Nature Genetics, 11, 402-408 (1995).
online README file
EJ Chesler, J Wang, L Lu, Y Qu, KF Manly, RW Williams (2003),
"Genetic correlates of gene expression in recombinant inbred strains: a
relational model system to explore neurobehavioral phenotypes",
Neuroinformatics, 1(4):343-357.