Tools   Select Another Resource Report Type

https://www.dynacom.co.jp/english/product/snpalyze_e/

Software application (entry from Genetic Analysis Software)

Proper citation: SNPALYZE (RRID:SCR_009401) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/GlfSingle

Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software)

Proper citation: GLFSINGLE/GLFTRIO/GLFMULTIPLES (RRID:SCR_013128) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/ggsd/

Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software)

Proper citation: GGSD (RRID:SCR_013129) Copy   

•   Source: SciCrunch Registry

http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/chromscan/

A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software)

Proper citation: CHROMSCAN (RRID:SCR_013131) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/eathomp/Anonftp/PANGAEA/BOREL/

Software application for inference of genealogical relationships from genetic data, including sibship inference.

Proper citation: BOREL (RRID:SCR_013135) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

•   Source: SciCrunch Registry

http://dlin.web.unc.edu/software/SNPMStat/

A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software)

Proper citation: SNPMSTAT (RRID:SCR_013339) Copy   

•   Source: SciCrunch Registry

http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm

Software application (entry from Genetic Analysis Software)

Proper citation: MECPM (RRID:SCR_013341) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/yli/whait/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software).

Proper citation: WHAIT (RRID:SCR_009425) Copy   

•   Source: SciCrunch Registry

http://www.molecular-haplotype.org/zaplo/zaplo_index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.

Proper citation: ZAPLO (RRID:SCR_009426) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: UNKNOWN (RRID:SCR_009423) Copy   

•   Source: SciCrunch Registry

http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software)

Proper citation: TFPGA (RRID:SCR_009421) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/MAOS/

Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)

Proper citation: MAOS (RRID:SCR_013351) Copy   

•   Source: SciCrunch Registry

http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

Proper citation: ANTMAP (RRID:SCR_013426) Copy   

•   Source: SciCrunch Registry

http://www.gridqtl.org.uk/

Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)

Proper citation: GRIDQTL (RRID:SCR_013397) Copy   

•   Source: SciCrunch Registry

http://vipbg.vcu.edu/vipbg/trimhap//

Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)

Proper citation: TRIMHAP (RRID:SCR_013512) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry