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http://ihg.gsf.de/cgi-bin/hw/hwa1.pl (testing part)

Software application that tests for deviation from Hardy-Weinberg equilibrium and tests for association in case controls studies; Plot genotype frequencies graphically using a de Finetti diagram. (entry from Genetic Analysis Software)

Proper citation: FINETTI (RRID:SCR_009179) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/linkage_utils/ceph2cri/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to convert output from CEPH DBMS to CRIMAP format.

Proper citation: CEPH2CRI (RRID:SCR_009143) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/h-1.html#homoghomogm

Software application (entry from Genetic Analysis Software)

Proper citation: HOMOG/HOMOGM (RRID:SCR_009237) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~mfarrall/twoloc.htm

Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)

Proper citation: TWOLOC (RRID:SCR_009230) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap/

Software application for conversion of LINKAGE format data files to CRI-MAP format (entry from Genetic Analysis Software)

Proper citation: LNKTOCRI (RRID:SCR_009256) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/SLINK.htm

Software application (entry from Genetic Analysis Software)

Proper citation: SLINK (RRID:SCR_009397) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: UTIL (RRID:SCR_009424) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/l/linkage---ceph/

Software application (entry from Genetic Analysis Software)

Proper citation: LINKAGE - CEPH (RRID:SCR_007048) Copy   

•   Source: SciCrunch Registry

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

A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping. (entry from Genetic Analysis Software)

Proper citation: MAP MANAGER QT (RRID:SCR_008101) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/t-1.html#tlinkage

Software programs that are extensions of the LINKAGE programs that allow the disease phenotype to be under the control of disease two loci. (entry from Genetic Analysis Software)

Proper citation: TLINKAGE (RRID:SCR_008838) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: EH (RRID:SCR_009168) 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

https://epi.mdanderson.org/~xzhou/Software/Linkage_imprinting/

Software application that is a parametric model-based approach to analyzing pedigree data for genomic imprinting. They have modified widely used LINKAGE program to incorporate imprinting. In addition, the LINKAGE-IMPRINT program allows for the use of sex-specific recombination in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. (entry from Genetic Analysis Software)

Proper citation: LINKAGE-IMPRINT (RRID:SCR_009253) Copy   

•   Source: SciCrunch Registry

https://www.wur.nl/en/show/SMOOTH.htm

Software tool that recognises and removes the most unrealistic data pointsfor the construction of accurate linkage maps, which is not so much depending on the quality of the mapping software, but mostly on the marker data quality. Missing values and scoring errors can severely influence the calculated marker order. This software was used to construct the 10,000 marker potato map. The removal of improbable data point is a good medicine for linkage maps, that is not easily overdosed. One error is more harmfull than ten missing values. The software was never intended as user-friendly software. In these days it would be more useful to re-do the programming of the pascal source code into a perl script. Anyone who takes the initiative to generate such a script is welcomed to contact the authors. SMOOTH works best in close cooperation with mapping algorithm RECORD (entry from Genetic Analysis Software)

Proper citation: SMOOTH (RRID:SCR_009398) Copy   

•   Source: SciCrunch Registry

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

Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)

Proper citation: SIMULATE (RRID:SCR_009391) Copy   

•   Source: SciCrunch Registry