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http://www.reading.ac.uk/Statistics/genetics/software.html

Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software)

Proper citation: HWMET (RRID:SCR_013480) Copy   

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http://pga.gs.washington.edu/VH1.html

Software application for displaying estimated haplotype data (entry from Genetic Analysis Software)

Proper citation: VH (RRID:SCR_013402) Copy   

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

A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software)

Proper citation: ECLIPSE (RRID:SCR_013130) Copy   

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http://csg.sph.umich.edu//abecasis/GRR/

A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)

Proper citation: GRR (RRID:SCR_013496) Copy   

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

Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)

Proper citation: PEDFIDDLER (RRID:SCR_013376) Copy   

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http://pga.gs.washington.edu/VG2.html

Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)

Proper citation: VG (RRID:SCR_013378) Copy   

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

A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)

Proper citation: TAGIMPUTE (RRID:SCR_013338) Copy   

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http://www.dynacom.co.jp/u-tokyo.ac.jp/snphitlink/

Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)

Proper citation: SNP HITLINK (RRID:SCR_013340) Copy   

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http://software.bfh-inst2.de/download3.html

Software application (entry from Genetic Analysis Software)

Proper citation: SGS (RRID:SCR_013460) Copy   

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

A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)

Proper citation: AUTOSCAN (RRID:SCR_013510) Copy   

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http://www.stats.ox.ac.uk/%7Emarchini/software.html

An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)

Proper citation: POPGEN (RRID:SCR_007315) Copy   

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https://www.nugene.org/

Collects and stores genetic (DNA) samples along with associated healthcare information from patients of Northwestern-affiliated hospitals and clinics. This resource is available to scientists to conduct groundbreaking genetic research. The information and blood samples provided will be used by researchers to examine the role genes play in the development and treatment of common diseases. The NUgene Project seeks to increase the understanding of genetic mechanisms underlying common diseases, assist in the development of DNA-based technology for diagnosis and treatment of disease, and aid physicians and other healthcare providers in the application of genetics to the practice of medicine. NUgene participants are recruited throughout the Northwestern-affiliated healthcare community in order to create an ethnically and medically diverse population for research. Participants must be 18 years of age or older and receive their medical care from a Northwestern-affiliated provider, regardless of health status. Consenting individuals complete all aspects of enrollment in a single meeting with a research coordinator. The enrollment process includes the donation of a single sample of blood and the completion of a self-administered questionnaire. Participants also sign a consent form during this encounter. The NUgene Project is an interdisciplinary project that relies on the expertise of individuals working in a variety of fields, including science, medicine, clinical research, statistics, epidemiology, and computational biology. NUgene''s multidisciplinary approach has spurred collaborations within Northwestern-affiliated institutions and with other outside institutions. This collaboration of ideas is the future of genetics and genomic research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NUgene Project (RRID:SCR_007426) Copy   

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http://www.stats.ox.ac.uk/~mcvean/LDhat/

Software package for the analysis of recombination rates from population genetic data (entry from Genetic Analysis Software)

Proper citation: LDHAT (RRID:SCR_006298) Copy   

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https://varscan.sourceforge.net/

Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software).

Proper citation: VarScan (RRID:SCR_006849) Copy   

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The record is no longer available at this source.

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

Proper citation: LSP (RRID:SCR_007059) Copy   

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http://bios.ugr.es/~mabad/rTDT/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: RTDT (RRID:SCR_007336) Copy   

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http://www.hpcf.upr.edu/~humberto/software/TkMap/

Software program for drawing genetic maps (entry from Genetic Analysis Software)

Proper citation: TKMAP (RRID:SCR_007457) Copy   

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http://www.stat.cmu.edu/~roeder/=ettdt/

Software application (entry from Genetic Analysis Software)

Proper citation: ET-TDT (RRID:SCR_007657) Copy   

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http://www.people.fas.harvard.edu/~junliu/BEAM/

Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software)

Proper citation: BEAM (RRID:SCR_007258) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry