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http://www.stsiweb.org/infrastructure/software_data/snp_expectation_maximization_snpem/

Software application for EM algorithm estimations of SNP haplotypes (entry from Genetic Analysis Software)

Proper citation: SNPEM (RRID:SCR_009086) Copy   

•   Source: SciCrunch Registry

http://hasstedt.genetics.utah.edu/

Software application that can (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models (entry from Genetic Analysis Software)

Proper citation: PAP (RRID:SCR_009083) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/qin/FESTA/

Software application (entry from Genetic Analysis Software)

Proper citation: FESTA (RRID:SCR_009081) Copy   

•   Source: SciCrunch Registry

http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: EHPLUS (RRID:SCR_009159) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/jattwood/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for detecting and displaying well-characterized meiotic breakpoints in human family data.

Proper citation: CROSSFIND (RRID:SCR_009157) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimappvm.shtml

Software application that is a parallel version of CRIMAP (entry from Genetic Analysis Software)

Proper citation: CRIMAP-PVM (RRID:SCR_009156) Copy   

•   Source: SciCrunch Registry

http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm

A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. (entry from Genetic Analysis Software)

Proper citation: CHROMOSEG (RRID:SCR_009152) Copy   

•   Source: SciCrunch Registry

http://coding.plantpath.ksu.edu/~jcn/MatLink.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A MATLAB utility for estimating genetic linkage in exotic line-cross mating designs.

Proper citation: MATLINK (RRID:SCR_009148) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application to detect genetically abnormal subjects in a case-control sample based on genotypes at multiple marker loci. (entry from Genetic Analysis Software)

Proper citation: CHECKHET (RRID:SCR_009147) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/linkage_utils/ceph2cri/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to convert output from CEPH DBMS to CRIMAP format.

Proper citation: CEPH2CRI (RRID:SCR_009143) Copy   

•   Source: SciCrunch Registry

http://www.stat.uchicago.edu/~mcpeek/software/CCQLSpackage1.3/

Software application (entry from Genetic Analysis Software)

Proper citation: CC-QLS (RRID:SCR_009140) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/rarevariant/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2026. Software application for 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. (entry from Genetic Analysis Software)

Proper citation: CCRAVAT (RRID:SCR_009141) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~marchini/software.html

A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)

Proper citation: GWAPOWER (RRID:SCR_009216) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/21/24/4430/180359

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 7,2025. Software application that is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included. (entry from Genetic Analysis Software)

Proper citation: GSMA (RRID:SCR_009214) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/chen/ghost/

Software package for family-based genomewide association (GWA) analysis, with the ability to infer missing genotypes using the Elston-Stewart algorithm. When SNPs from an association panel are less complete (i.e., having more missing genotypes) than markers from a linkage panel, many of the missing genotypes can be determined. GHOST can handle large pedigrees -- when pedigrees are small, Merlin is also recommended for this analysis. (entry from Genetic Analysis Software)

Proper citation: GHOST (RRID:SCR_009209) Copy   

•   Source: SciCrunch Registry

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

Software application for analysis and manipulation of genetic linkage data of genetic linkage data, including conversions of pedigree files between CRI-MAP and LINKAGE format. (entry from Genetic Analysis Software)

Proper citation: GENTOOLS (RRID:SCR_009205) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/~ukai/gest98.html

Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GEST (RRID:SCR_009206) Copy   

•   Source: SciCrunch Registry

http://www.genoproof.com or http://qualitype.de/genoproof/

Software package for the analysis of multiplex PCR kits within the scope of paternity testing, kinship cases and population studies. GenoProof offers: (1) probably the most extensive existing population database for all supported markers of more than 50 ethnic groups, (2) individually configurable quality assurance options, (3) complex concept of user rights in order to guarantee data security, (4) languages German and English (entry from Genetic Analysis Software)

Proper citation: GENOPROOF (RRID:SCR_009204) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/genevar/

A database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies. Genevar allows researchers to investigate eQTL (expression quantitative trait loci) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the internet via web services protocols. (entry from Genetic Analysis Software)

Proper citation: GENEVAR (RRID:SCR_009201) Copy   

•   Source: SciCrunch Registry