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http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

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http://dlin.web.unc.edu/software/SCORE-Seq/

A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)

Proper citation: SCORE-SEQ (RRID:SCR_013121) Copy   

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http://www.aps.uoguelph.ca/~msargol/qmsim/

Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)

Proper citation: QMSIM (RRID:SCR_013123) Copy   

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https://www.genetics.ucla.edu/software/download?package=4

Software application for analysis of sperm typing data. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPERM (RRID:SCR_009409) Copy   

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http://www.nitrc.org/projects/se_linux/

Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data

Proper citation: Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) Copy   

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https://www.dynacom.co.jp/english/product/snpalyze_e/

Software application (entry from Genetic Analysis Software)

Proper citation: SNPALYZE (RRID:SCR_009401) Copy   

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http://perlprimer.sourceforge.net/

A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

Proper citation: PerlPrimer (RRID:SCR_012038) Copy   

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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   

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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   

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http://simupop.sourceforge.net

A forward-based population genetics simulation program capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it. (entry from Genetic Analysis Software)

Proper citation: SIMUPOP (RRID:SCR_009392) Copy   

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http://brainhealthregistry.org/

A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games).

Proper citation: Brain Health Registry (RRID:SCR_010230) Copy   

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http://www.molecular-haplotype.org/zaplo/zaplo_index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.

Proper citation: ZAPLO (RRID:SCR_009426) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: UNKNOWN (RRID:SCR_009423) Copy   

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http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software)

Proper citation: TFPGA (RRID:SCR_009421) Copy   

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http://www.stat.ohio-state.edu/~statgen/SOFTWARE/SIMPLE/

Software application that calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation. (entry from Genetic Analysis Software)

Proper citation: SIMPLE (RRID:SCR_009389) Copy   

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http://csg.sph.umich.edu/boehnke/simlink.php

Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)

Proper citation: SIMLINK (RRID:SCR_009387) Copy   

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http://dmpi.duke.edu/simla-simulation-software-version-32

SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software)

Proper citation: SIMLA (RRID:SCR_009385) Copy   

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https://github.com/emsweene/SuBLIME_package

Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available.

Proper citation: SuBLIME (RRID:SCR_014409) Copy   

•   Source: SciCrunch Registry

https://www.qimacros.com/spc-software-for-excel/

A statistical process control (SPC) add-in for Microsoft Excel. The user can select their data and the program will draw the desired chart or run the desired statistical test.

Proper citation: QI Macros (RRID:SCR_014496) Copy   

•   Source: SciCrunch Registry

http://www.edanzediting.com/journal_advisor

A training service which offers English editorial support for primarily non-native English speaking scientific researchers. Users answer a questionairre concerning their progress with their manuscript and Edanz suggests which of its services users should utilize. Services include Journal Advisor, English Editing, Expert Scientific Review, Cover Letter Development, Review Editing, Abstract Development, Response Letter Edit and Manuscript Check, Author-guided Rewriting, and Reviewer Recommendation. Edanz also offers training workshops and seminars for non-native English speakers.

Proper citation: Edanz's journal advisor (RRID:SCR_014013) Copy   

•   Source: SciCrunch Registry