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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

http://research.nhgri.nih.gov/software/TRAP/

Software tool for determining a regression model of quantitative or binary trait variation when the number of possible genetic predictors is very large, considering only a moderate number of predictors at one time, using unrelated or family data. (entry from Genetic Analysis Software)

Proper citation: TRAP (RRID:SCR_009002) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/mgamapf2/

Software application that map QTLs in F-2 intercross in model organisms (entry from Genetic Analysis Software)

Proper citation: MGA-MAPF2 (RRID:SCR_008108) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting (entry from Genetic Analysis Software)

Proper citation: ILR (RRID:SCR_007895) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/2SNP.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.

Proper citation: 2SNP (RRID:SCR_009038) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.

Proper citation: AGEINF (RRID:SCR_009039) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Albert/albert.shtml

Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software)

Proper citation: ALBERT (RRID:SCR_009037) 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://www.epigenetic.org/Linkage/act.html,

Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software)

Proper citation: ACT (RRID:SCR_009033) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)

Proper citation: S (RRID:SCR_007646) Copy   

•   Source: SciCrunch Registry

http://www.chgb.org.cn/lda/lda.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A Java program for analyzing the pairwise linkage disequilibrium.

Proper citation: LDA (RRID:SCR_007527) Copy   

•   Source: SciCrunch Registry

http://www-gene.cimr.cam.ac.uk/clayton/software/

Software program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects (entry from Genetic Analysis Software)

Proper citation: SNPHAP (RRID:SCR_008456) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/simcoal/

Software application (entry from Genetic Analysis Software)

Proper citation: SIMCOAL (RRID:SCR_008450) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/RvTests

Software application (entry from Genetic Analysis Software)

Proper citation: RVTESTS (RRID:SCR_007639) 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

http://www.cs.helsinki.fi/group/genetics/haplotyping.html

Software application for population-based haplotyping (entry from Genetic Analysis Software)

Proper citation: HAPLOREC (RRID:SCR_009055) 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.columbia.edu/~ws2267/SOFT/EAGLET/eaglet.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location.

Proper citation: EAGLET (RRID:SCR_009166) Copy   

•   Source: SciCrunch Registry

http://nephrologie.uniklinikum-leipzig.de/nephrologie.site,postext,easylinkage.html

Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies.

Proper citation: EASYLINKAGE/EASYLINKAGE-PLUS (RRID:SCR_009167) Copy   

•   Source: SciCrunch Registry

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

Software application that is similar to the BPPH program (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DPPH (RRID:SCR_009164) Copy   

•   Source: SciCrunch Registry