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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   

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.

Proper citation: INTEGRAYEDMAP (RRID:SCR_007489) Copy   

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http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

Proper citation: LDMAP (RRID:SCR_006308) Copy   

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http://krunch.med.yale.edu/haplo/

Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 2 (RRID:SCR_009059) Copy   

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https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

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http://dceg.cancer.gov/tools/design/power

Windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions). (entry from Genetic Analysis Software)

Proper citation: POWER (RRID:SCR_009057) Copy   

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http://www.jenti.org

An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way. (entry from Genetic Analysis Software)

Proper citation: JENTI (RRID:SCR_009053) Copy   

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

Software application designed for the construction of highly saturated linkage maps, based on BC1, DH, Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supported. (entry from Genetic Analysis Software)

Proper citation: COMBIN (RRID:SCR_009050) Copy   

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http://cmpg.unibe.ch/software/arlequin3/

An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)

Proper citation: ARLEQUIN (RRID:SCR_009051) Copy   

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

Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood. (entry from Genetic Analysis Software)

Proper citation: GRONLOD (RRID:SCR_009049) Copy   

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http://www.biodata.ee/SNPassistant.htm (30 days trial version)

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects.

Proper citation: SNP ASSISTANT (RRID:SCR_009048) Copy   

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