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http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Software application for genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. (entry from Genetic Analysis Software)

Proper citation: FISHER (RRID:SCR_009181) Copy   

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http://embio.yonsei.ac.kr/haplowser/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOWSER (RRID:SCR_009095) 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://genome.sph.umich.edu/wiki/UMAKE

Software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies. (entry from Genetic Analysis Software)

Proper citation: UMAKE (RRID:SCR_009093) Copy   

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http://www.cnrs-gif.fr/pge/bioinfo/lea/index.php?lang=en

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

Proper citation: LEA (RRID:SCR_009090) Copy   

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http://www.sph.umich.edu/csg/abecasis/Exact/index.html

Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)

Proper citation: SNP-HWE (RRID:SCR_008555) 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://watson.hgen.pitt.edu/register/soft_doc.html,

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that calculates likelihood on pedigrees (entry from Genetic Analysis Software)

Proper citation: VITESSE (RRID:SCR_009089) Copy   

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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   

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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   

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

Software application (entry from Genetic Analysis Software)

Proper citation: FESTA (RRID:SCR_009081) Copy   

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http://www.cs.cmu.edu/~genome/FAST-MAP.html

Fluorescent allele-calling software toolkit: a computer software for fully automated microsatellite genotyping. (entry from Genetic Analysis Software)

Proper citation: FASTMAP (1) (RRID:SCR_008346) Copy   

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http://www.molecular-haplotype.org/profiler/profiler_intro.htm

A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PROFILER (RRID:SCR_009339) Copy   

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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   

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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   

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

Software application that is part of the LINKAGE auxiliary program (entry from Genetic Analysis Software)

Proper citation: PREPLINK (RRID:SCR_009335) Copy   

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http://fisher.utstat.toronto.edu/sun/Software/Prest or previously, http://galton.uchicago.edu/~mcpeek/software/prest

Software program that detects pedigree errors in general outbred pedigrees by use of genome-screen data. When a potential pedigree error is detected, our companion program, ALTERTEST, determines which relationships are compatible with the observed genotype data. Both programs are freely available on the web. (entry from Genetic Analysis Software)

Proper citation: PREST (RRID:SCR_009336) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Excel spreadsheet to calculate power of affected sibpairs and TDT analyses (entry from Genetic Analysis Software)

Proper citation: POWTEST (RRID:SCR_009334) Copy   

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http://www.geneticepi.com/Research/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: POOL STR (RRID:SCR_009331) 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   

•   Source: SciCrunch Registry