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http://pritchardlab.stanford.edu/software.html

Software application that is a companion program to STRUCTURE that is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. (entry from Genetic Analysis Software)

Proper citation: STRAT (RRID:SCR_009110) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/prastas/haplovisual/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOVISUAL (RRID:SCR_009073) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/becker.html

Software application for haplotype association analysis of unphased genotype data. It can be used both for population data (case-control) and nuclear family data. The program is optimized for haplotype frequency estimation with the EM-algorithm for many markers. FAMHAP provides a method which searches for potential genotyping errors and several tests for haplotype-based association analysis. Particular emphasis is on Monte-Carlo simulations, which are necessary in the context of haplotype association, where asymptotic theory often fails, and in the context of multiple testing problems. (entry from Genetic Analysis Software)

Proper citation: FAMHAP (RRID:SCR_009070) Copy   

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http://www.rni.helsinki.fi/~mjs/

Software application to select a trait-associated subset of markers among many candidates. The program is based on Bayesian modeling/estimation and it suits for both quantitative and qualitative traits. It can handle bi- and multiallelic markers as well as applied in situations where part of the marker genotypes may be missing. As an output of the program, one obtains posterior estimate of number and positions of trait-associated markers. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BAMA (RRID:SCR_009071) Copy   

•   Source: SciCrunch Registry

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

Markov chain Monte Carlo program for association in two-dimensional contingency tables, and for testing Hardy-Weinberg equilibrium. (entry from Genetic Analysis Software)

Proper citation: HARDY (RRID:SCR_009107) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/~clange/default.htm

An interactive software package that provides tools for the design and the data analysis of family-based association studies. (entry from Genetic Analysis Software)

Proper citation: PBAT (RRID:SCR_009105) Copy   

•   Source: SciCrunch Registry

http://www.statistics.com/software-directory/helixtree

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

Proper citation: HELIXTREE (RRID:SCR_009067) Copy   

•   Source: SciCrunch Registry

http://www.molecular-haplotype.org/finesse/finesse_intro.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to incorporate regressive models into the VITESSE likelihood engine.

Proper citation: FINESSE (RRID:SCR_009100) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016.

Proper citation: SVCC (RRID:SCR_009068) Copy   

•   Source: SciCrunch Registry

http://www.montpellier.inra.fr/URLB/

Software application employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). (entry from Genetic Analysis Software)

Proper citation: GENECLASS (RRID:SCR_009065) Copy   

•   Source: SciCrunch Registry

http://www.statgen.org/main/index.php/Downloads/Downloads

Software application that aims to speed up the preparation of linkage data files passed on to the Alohomora software for data from the Affymetrix or Illumina assays. Chip2Spell gathers the information necessary to supplement the genotype data (such as the genetic map of the markers and the population-specific allele frequencies) from publicly available annoation files from Affymetrix and Illumina. The program formats the genotype data for input into the Alohomora program. (entry from Genetic Analysis Software)

Proper citation: CHIP2SPELL (RRID:SCR_009060) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ebc.ee/download/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Robust haploblock border reliability estimation tool implemented for LD based haploblock detection method. The most important new features are bootstrapping and overlapping block borders. (entry from Genetic Analysis Software)

Proper citation: BOOSTRAPPER (RRID:SCR_009135) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A set of programs for calculations under different linkage disequilibrium (LD) distribution models (entry from Genetic Analysis Software)

Proper citation: BOOLD (RRID:SCR_009134) Copy   

•   Source: SciCrunch Registry

http://www.rockefeller.edu/biolad-db/

Software application that is a research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password protected BiolAD-DB SQL compliant server database. BiolAD-DB tools further provide functionalities for generating customized reports and views. (entry from Genetic Analysis Software)

Proper citation: BIOLAD-DB (RRID:SCR_009131) Copy   

•   Source: SciCrunch Registry

http://www.htbiology.com/software.php

Collection of data analysis tools and interrelated biomedical information in a single easy-to-use software package that includes a component-based software/data integration platform that can quickly transform fragmented enterprise legacy data and software into an integrated suite of tools and knowledge base to achieve maximal usability, interoperability, scalability, and extensibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BIOIDE (RRID:SCR_009130) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOWSER (RRID:SCR_009095) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/

Software applications including ASP, a power calculator for gene mapping using a sibpair design (concordant or discordant) and ASPSHARE, which complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. (entry from Genetic Analysis Software)

Proper citation: ASP/ASPSHARE (RRID:SCR_009128) Copy   

•   Source: SciCrunch Registry