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http://systemsbio.ucsd.edu/GoSurfer/

GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible

Proper citation: GoSurfer (RRID:SCR_005789) Copy   

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http://mga.bionet.nsc.ru/soft/pedpeel/

Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software)

Proper citation: PEDPEEL (RRID:SCR_008436) Copy   

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

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

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http://mga.bionet.nsc.ru/soft/index.html

Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software)

Proper citation: PEDIGREEQUERY (RRID:SCR_009041) Copy   

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http://watson.hgen.pitt.edu/register/soft_doc.html

Software application that is a faster version of SLINK (entry from Genetic Analysis Software)

Proper citation: FASTSLINK (RRID:SCR_008664) Copy   

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https://github.com/gaow/genetic-analysis-software/blob/master/pages/MOSCPHASER.md

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.

Proper citation: MOSCPHASER (RRID:SCR_009092) Copy   

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http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

Proper citation: ADMIXMAP (RRID:SCR_009035) Copy   

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https://github.com/gaow/genetic-analysis-software/blob/master/pages/GLUE.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GLUE (RRID:SCR_009211) Copy   

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http://www.well.ox.ac.uk/~mfarrall/twoloc.htm

Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)

Proper citation: TWOLOC (RRID:SCR_009230) Copy   

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http://www.daimi.au.dk/~mailund/GeneRecon/

Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)

Proper citation: GENERECON (RRID:SCR_009195) Copy   

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http://statgen.ncsu.edu/zaykin/htr.html

Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software)

Proper citation: HTR (RRID:SCR_009241) Copy   

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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.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   

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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   

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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   

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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

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   

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https://www.hsph.harvard.edu/skat/

Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software)

Proper citation: SKAT (RRID:SCR_009396) 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   

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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