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http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ldb;

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software)

Proper citation: LDB/LDB+ (RRID:SCR_000839) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/jattwood/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for detecting and displaying well-characterized meiotic breakpoints in human family data.

Proper citation: CROSSFIND (RRID:SCR_009157) Copy   

•   Source: SciCrunch Registry

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

Software application that is a modification of the GENEHUNTER software package (version 1.3)that allows users to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect. (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-IMPRINTING (RRID:SCR_009192) Copy   

•   Source: SciCrunch Registry

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

Software application for complex segregation analysis with the mixed model (major locus and polygenes). (entry from Genetic Analysis Software)

Proper citation: POINTER (RRID:SCR_009330) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/software/simwalk

Software programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method. (entry from Genetic Analysis Software)

Proper citation: SIMWALK (RRID:SCR_009393) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)

Proper citation: COMDS (RRID:SCR_000832) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html,

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that assigns each person the haplotype with the highest conditional probability using Elston-Stewart algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 1 (RRID:SCR_009058) 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://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.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   

•   Source: SciCrunch Registry

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

Software application for multiple pairwise linkage analysis under interference (entry from Genetic Analysis Software)

Proper citation: MAP/MAP+/MAP+H/MAP2000 (RRID:SCR_009272) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu/boehnke/simlink.php

Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)

Proper citation: SIMLINK (RRID:SCR_009387) Copy   

•   Source: SciCrunch Registry

https://watson.hgen.pitt.edu/docs/splink108.html

Software application for linkage analysis using affected sib pairs (entry from Genetic Analysis Software)

Proper citation: SPLINK (RRID:SCR_009414) Copy   

•   Source: SciCrunch Registry

http://www.joslinresearch.org/LabSites/Krolewski/splat/

Software application that can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPLAT (RRID:SCR_009411) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

•   Source: SciCrunch Registry