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https://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html

Software application allowing to simulate population genetics datasets. It allows generating genetic data for haploid, diploid, and haplodiploid organisms under a variety of mating systems. It includes various migration and mutation models. Output can be generated for the FSTAT, GENEPOP, and ARLEQUIN genetic analysis packages. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EASYPOP (RRID:SCR_008961) Copy   

•   Source: SciCrunch Registry

http://www.inra.fr/mia/T/CarthaGene/

A genetic/radiation hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms inspired from TSP (Traveling Salesman Problem) technology. It can handle large data sets made up of different populations (either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds, haploid/diploid radiation hybrids). It can also exploit existing syntenic relationships between the organism mapped and a reference (sequenced) organism for accurate dense RH mapping. (entry from Genetic Analysis Software)

Proper citation: CARTHAGENE (RRID:SCR_009013) Copy   

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http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi

Software package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCKFINDER (RRID:SCR_005844) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/Exact/index.html

Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)

Proper citation: SNP-HWE (RRID:SCR_008555) Copy   

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

Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software)

Proper citation: PEDPEEL (RRID:SCR_008436) Copy   

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http://www.sph.umich.edu/csg/liang/genome/

Software application to simulate sequences drawn from a population under the Wright-Fisher neutral model. The purpose of this program is to simulate sequences on the whole genome scale within practical time. (entry from Genetic Analysis Software)

Proper citation: GENOME (RRID:SCR_008949) Copy   

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http://www.stat.cmu.edu/~roeder/=ettdt/

Software application (entry from Genetic Analysis Software)

Proper citation: ET-TDT (RRID:SCR_007657) Copy   

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http://www.cs.cmu.edu/~genome/FAST-MAP.html

Fluorescent allele-calling software toolkit: a computer software for fully automated microsatellite genotyping. (entry from Genetic Analysis Software)

Proper citation: FASTMAP (1) (RRID:SCR_008346) Copy   

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http://www-rcf.usc.edu/~stram/tagSNPs.html

Software application (entry from Genetic Analysis Software)

Proper citation: TAGSNP (RRID:SCR_008623) Copy   

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http://www.people.fas.harvard.edu/~junliu/BEAM/

Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software)

Proper citation: BEAM (RRID:SCR_007258) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/ldSelect.html

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.

Proper citation: INTEGRAYEDMAP (RRID:SCR_007489) Copy   

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

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

Proper citation: LDMAP (RRID:SCR_006308) Copy   

•   Source: SciCrunch Registry

http://krunch.med.yale.edu/haplo/

Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 2 (RRID:SCR_009059) Copy   

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https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

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http://dceg.cancer.gov/tools/design/power

Windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions). (entry from Genetic Analysis Software)

Proper citation: POWER (RRID:SCR_009057) Copy   

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http://www.jenti.org

An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way. (entry from Genetic Analysis Software)

Proper citation: JENTI (RRID:SCR_009053) Copy   

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

Software application designed for the construction of highly saturated linkage maps, based on BC1, DH, Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supported. (entry from Genetic Analysis Software)

Proper citation: COMBIN (RRID:SCR_009050) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/arlequin3/

An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)

Proper citation: ARLEQUIN (RRID:SCR_009051) Copy   

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

Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood. (entry from Genetic Analysis Software)

Proper citation: GRONLOD (RRID:SCR_009049) Copy   

•   Source: SciCrunch Registry