Tools   Select Another Resource Report Type

http://www.chg.duke.edu/research/simla30.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

Proper citation: SIMULA (RRID:SCR_009390) Copy   

•   Source: SciCrunch Registry

http://magnet.c2b2.columbia.edu/mutagenesys/

Software application that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: HapMap, whole-genome marker correlation data, and OMIM database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. (entry from Genetic Analysis Software)

Proper citation: MUTAGENESYS (RRID:SCR_009309) Copy   

•   Source: SciCrunch Registry

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER/OUTBRED (RRID:SCR_009306) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/multiPopTagSelect.html

Software program that selects a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. (entry from Genetic Analysis Software)

Proper citation: MULTIPOPTAGSELECT (RRID:SCR_009307) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/multidiseq/

A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software)

Proper citation: MULTIDISEQ (RRID:SCR_009304) Copy   

•   Source: SciCrunch Registry

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER (RRID:SCR_009305) Copy   

•   Source: SciCrunch Registry

http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm

A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software)

Proper citation: MPDA (RRID:SCR_009303) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.org/simped/

Software 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. (entry from Genetic Analysis Software)

Proper citation: SIMPED (RRID:SCR_009388) Copy   

•   Source: SciCrunch Registry

http://www.flintbox.com/public/project/500/

Software application 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 (entry from Genetic Analysis Software)

Proper citation: SNP CHART (RRID:SCR_009386) Copy   

•   Source: SciCrunch Registry

http://www.gohad.uwa.edu.au/software/simhap

Software application providing a comprehensive modelling framework and a multiple-imputation approach to haplotypic analysis of population-based data. It 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. (entry from Genetic Analysis Software)

Proper citation: SIMHAP (RRID:SCR_009384) Copy   

•   Source: SciCrunch Registry

https://genepi.qimr.edu.au/staff/davidD/#sib-pair

Software program that 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. (entry from Genetic Analysis Software)

Proper citation: SIB-PAIR (RRID:SCR_009382) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/siblink-v-30

Software application that 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. (entry from Genetic Analysis Software)

Proper citation: SIBLINK (RRID:SCR_009381) Copy   

•   Source: SciCrunch Registry

http://archive.broadinstitute.org/mpg/sweep/

Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software)

Proper citation: SWEEP (RRID:SCR_009418) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/sumstat.html

Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software)

Proper citation: SUMSTAT (RRID:SCR_009416) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as 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 trait locus. entry from Genetic Analysis Software.

Proper citation: SUP (RRID:SCR_009417) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/epidemiology/tagster/

Software tool to select, evaluate and visualize LD tag SNPs for single or multiple populations. The input files can be a set of dumped genotype files from International HapMap Project (http://www.hapmap.org/) (Hapmap format) or Seattle SNPs (http://pga.gs.washington.edu/) (Prettybase format). The ouput is a set of LD tag SNPs for single or multiple populations. (entry from Genetic Analysis Software)

Proper citation: TAGSTER (RRID:SCR_009413) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml

Collection of nine software packages for genetic analysis: BOREL, HARDY, MORGAN (now 2 and 3), Pedpack, InSegT, Loki, MCLEEPS, Pedfiddler, and Eclipse.

Proper citation: PANGAEA (RRID:SCR_013119) Copy   

•   Source: SciCrunch Registry

http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software)

Proper citation: SASGENE (RRID:SCR_013084) Copy   

•   Source: SciCrunch Registry

http://www.adfg.alaska.gov/index.cfm?adfg=fishinggeneconservationlab.software

Software application that 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. (entry from Genetic Analysis Software)

Proper citation: SPAM (RRID:SCR_009407) Copy   

•   Source: SciCrunch Registry

https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)

Proper citation: SNPTEST (RRID:SCR_009406) Copy   

•   Source: SciCrunch Registry