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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   

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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   

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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   

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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   

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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   

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

Software application (entry from Genetic Analysis Software)

Proper citation: BLADE (RRID:SCR_009132) Copy   

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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   

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http://www.plantbreeding.wur.nl/UK/software_record.html

Software application that can be used for the ordering of loci on genetic linkage maps. The method is based on minimisation of the total number of recombination events. Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Data files are .LOC JoinMap format. Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes. (entry from Genetic Analysis Software)

Proper citation: RECORD (RRID:SCR_009097) Copy   

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

Software program that computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors. (entry from Genetic Analysis Software)

Proper citation: TDT-AE (RRID:SCR_009094) Copy   

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https://github.com/genomizer/genomizer.github.io

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A platform independent Java program for the analysis of genome wide association experiments. (entry from Genetic Analysis Software).

Proper citation: GENOMIZER (RRID:SCR_009127) Copy   

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http://genepool.tgen.org/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. GenePool supports genotyping platforms from Affymetrix and Illumina.

Proper citation: GENEPOOL (RRID:SCR_009087) Copy   

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http://www.helsinki.fi/~tsjuntun/linkage/analyze/

A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)

Proper citation: ANALYZE (RRID:SCR_009120) Copy   

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http://www4.ncsu.edu/~jholland/Epistacy/epistacy.htm

Software application (entry from Genetic Analysis Software)

Proper citation: EPISTACY (RRID:SCR_009088) Copy   

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http://www.rqtl.org

Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software)

Proper citation: R/QTL (RRID:SCR_009085) Copy   

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http://hydra.usc.edu/GxE

Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software)

Proper citation: QUANTO (RRID:SCR_009084) Copy   

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

Software application for detecting recent effective population size reductions from allele data frequencies (entry from Genetic Analysis Software)

Proper citation: BOTTLENECK (RRID:SCR_009082) Copy   

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

Software application for semiparametric family-based association (entry from Genetic Analysis Software)

Proper citation: SQTDT/SPDT (RRID:SCR_009080) Copy   

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http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

THIS RESOURCE IS NO LOGER IN SERVICE. Documented on May 16,2023. A simple dBASE III program for the management of pedigree and locus data. It permits easy extraction of genetic data for use with MENDEL and FISHER. (entry from Genetic Analysis Software)

Proper citation: DGENE (RRID:SCR_009158) Copy   

•   Source: SciCrunch Registry