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

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/LAMP/

Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

Proper citation: LAMP (RRID:SCR_001740) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/software/syzygy/

A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)

Proper citation: SYZYGY (RRID:SCR_002157) 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

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

Software program that allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GREGOR (RRID:SCR_009165) Copy   

•   Source: SciCrunch Registry

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

Software application - part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

Proper citation: MAKEPED (RRID:SCR_009162) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that manage genetic data (entry from Genetic Analysis Software)

Proper citation: DOLINK (RRID:SCR_009163) Copy   

•   Source: SciCrunch Registry

http://kumasakanatsuhiko.jp/projects/disentangler/

Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)

Proper citation: DISENTANGLER (RRID:SCR_009161) 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