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http://www.jurgott.org/linkage/LinkagePC.html

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

Proper citation: MAKEPED (RRID:SCR_009162) 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 that manage genetic data (entry from Genetic Analysis Software)

Proper citation: DOLINK (RRID:SCR_009163) Copy   

•   Source: SciCrunch Registry

http://kumasakanatsuhiko.jp/projects/disentangler/

Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)

Proper citation: DISENTANGLER (RRID:SCR_009161) Copy   

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http://gmc.mdc-berlin.de/alohomora/

Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)

Proper citation: ALOHOMORA (RRID:SCR_009117) Copy   

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http://www.hgu.mrc.ac.uk/Softdata/ALP/

Microsoft Windows application designed to analyze microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer. (entry from Genetic Analysis Software)

Proper citation: ALP (RRID:SCR_009118) Copy   

•   Source: SciCrunch Registry

http://www.stat.uchicago.edu/~wen/tuna/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 22, 2016. Free software package for estimating allele frequencies for all the SNPs available in a population reference panel (e.g. HapMap data base) based on genotype data from a subset of markers (e.g. the Illumina HumanHap300 BeadChip SNP set) in a group of subjects (e.g. the cases in a case-control sample)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TUNA (RRID:SCR_009112) Copy   

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http://galton.uchicago.edu/genehunterplus

Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-PLUS (RRID:SCR_009193) Copy   

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http://www.biostat.jhsph.edu/~wmchen/gf.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.

Proper citation: GENEFINDER (RRID:SCR_009190) Copy   

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http://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html#c63682

Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait.

Proper citation: genehunter-imprinting (RRID:SCR_009104) Copy   

•   Source: SciCrunch Registry

http://www.angelfire.com/mn2/nath/gems.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.

Proper citation: GEMS (RRID:SCR_009188) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/genecounting-2-2-gene-counting-haplotype-analysis.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

Proper citation: GENECOUNTING (RRID:SCR_009189) Copy   

•   Source: SciCrunch Registry

http://episun7.med.utah.edu/~alun/gchap/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

Proper citation: GCHAP (RRID:SCR_009186) Copy   

•   Source: SciCrunch Registry

http://www.epicentersoftware.com/products.php

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors. (entry from Genetic Analysis Software)

Proper citation: GAP (RRID:SCR_009183) Copy   

•   Source: SciCrunch Registry

http://fmph.ucsd.edu/faculty/cberry/bqtl/

Software application for the mapping of genetic traits from line crosses and recombinant inbred lines. It performs (1) maximum likelihood estimation of multi-gene models; (2) Bayesian estimation of multi-gene models via Laplace Approximations; and (3) interval mapping and composite interval mapping of genetic loci (entry from Genetic Analysis Software)

Proper citation: BQTL (RRID:SCR_009137) Copy   

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http://gaow.github.io/genetic-analysis-software/d-1.html#dnabaser

Software tool for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DNABASER (RRID:SCR_009138) Copy   

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http://wwwcsif.cs.ucdavis.edu/~gusfield/bpph.html

Software application for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. (entry from Genetic Analysis Software)

Proper citation: BPPH (RRID:SCR_009136) Copy   

•   Source: SciCrunch Registry

http://www.cs.auc.dk/~claus/block.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that performs general pedigree analysis on a general pedigree with any number of loops. It also allows users to perform two-point linkage analysis on a general pedigree with an arbitrary number of alleles., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLOCK (RRID:SCR_009133) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. 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: QUTIE (RRID:SCR_009098) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/index1.html

Software application (entry from Genetic Analysis Software)

Proper citation: BLADE (RRID:SCR_009132) Copy   

•   Source: SciCrunch Registry

http://hg-wen.uchicago.edu/software.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Software application (entry from Genetic Analysis Software)

Proper citation: STEPC (RRID:SCR_009096) Copy   

•   Source: SciCrunch Registry