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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   

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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   

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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://chgr.mc.vanderbilt.edu/page/gist

Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.

Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

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Issue

https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry

https://sites.pitt.edu/~weeks/docs/SimIBD.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: SIMIBD (RRID:SCR_002094) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry

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   

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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://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) 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