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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application to calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent).

Proper citation: KIN (RRID:SCR_009047) Copy   

•   Source: SciCrunch Registry

http://www.hoschl.cz/faster/

Software application to reduce family members so the families can be used in GENEHUNTER program. FASTER eliminates the most redundant individuals according to the set of weights (preferences) (Age, Information about genetic Markers, etc.) The program has several features such as automatical reducement of branches without any affected individuals, etc. (entry from Genetic Analysis Software)

Proper citation: FASTER (RRID:SCR_009045) Copy   

•   Source: SciCrunch Registry

http://www.multiqtl.com/

Software application that integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data. (entry from Genetic Analysis Software)

Proper citation: MULTIQTL (RRID:SCR_009043) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~mcpeek/software/spermseg

Software application for analysis of segregation in single-sperm data (entry from Genetic Analysis Software)

Proper citation: SPERMSEG (RRID:SCR_009044) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: ALLASS (RRID:SCR_009040) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.

Proper citation: SIMULAPLOT (RRID:SCR_009079) 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   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)

Proper citation: CASPAR (RRID:SCR_009074) Copy   

•   Source: SciCrunch Registry

http://www.genenetwork.org/webqtl/main.py

An interactive web site useful for exploring the genetic modulation of thousands of phenotypes gathered over a 30-year period by hundreds of investigators using reference panels of recombinant inbred strains of mice. WebQTL includes dense error-checked genetic maps, as well as extensive gene expression data sets (Affymetrix) acquired across more than 35 strains of mice. WebQTL accepts user-entered traits for BXD, AXB/BXA, CXB, BXH, AKXD recombinant inbred strains. (entry from Genetic Analysis Software)

Proper citation: WEBQTL (RRID:SCR_009072) Copy   

•   Source: SciCrunch Registry

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

https://www.helmholtz-muenchen.de/ige/service/software-download/genehunter-modscore/index.html

Software application that is an extension of GENEHUNTER-IMPRINTING, based on the original GENEHUNTER version 2.1 release 6, that allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. As of version 2.0, it is possible to use sex-specific recombination frequencies. The genetic positions of markers can be automatically read from a publicly available genetic map. (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-MODSCORE (RRID:SCR_009069) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/software/mareymap/

Software application that is a meiotic recombination rate estimation program. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAREYMAP (RRID:SCR_009066) Copy   

•   Source: SciCrunch Registry

http://associationviewer.vital-it.ch/

A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software)

Proper citation: ASSOCIATIONVIEWER (RRID:SCR_009063) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that uses multilocus genotypic data to allocate individuals to their most likely source population.

Proper citation: WHICHRUN (RRID:SCR_009064) Copy   

•   Source: SciCrunch Registry

http://www.mapmanager.org/mmQTX.html

A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals. A completely rewritten cross-platform version of Map Manager QT with enhanced analysis functions. (entry from Genetic Analysis Software)

Proper citation: MAP MANAGER QTX (RRID:SCR_009061) Copy   

•   Source: SciCrunch Registry

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

Software tool for construction of genetic linkage maps and analyzing Mendelian phenotypes. (entry from Genetic Analysis Software)

Proper citation: G-MENDEL (RRID:SCR_009062) 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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry