Tools   Select Another Resource Report Type

http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm

Software tool for analyses of pooled DNA data (entry from Genetic Analysis Software)

Proper citation: PDA (RRID:SCR_009317) Copy   

•   Source: SciCrunch Registry

http://cougar.fhcrc.org/software.php

Software application that is a Windows-based system designed for pedigree data management, providing a graphical interface for pedigree construction and output. (entry from Genetic Analysis Software)

Proper citation: PDPSYS (RRID:SCR_009318) Copy   

•   Source: SciCrunch Registry

http://linkage.rockefeller.edu/pawe/

Software application for power and sample size calculations for genetic case-control association studies allowing for errors (entry from Genetic Analysis Software)

Proper citation: PAWE (RRID:SCR_009316) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers. (entry from Genetic Analysis Software)

Proper citation: NUCULAR (RRID:SCR_009311) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 29, 2016. A workbench tool to make existing population genetic software more accessible and to facilitate the integration of new tools for analyzing patterns of DNA sequence variation, within a phylogenetic context. Collectively, SNAP tools can serve as a bridge between theoretical and applied population genetic analysis. The exploration of DNA sequence variation for making inferences on evolutionary processes in populations requires the coordinated implementation of a Suite of Nucleotide Analysis Programs (SNAP), each bound by specific assumptions and limitations.

Proper citation: Suite of Nucleotide Analysis Programs (RRID:SCR_009399) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/SLINK.htm

Software application (entry from Genetic Analysis Software)

Proper citation: SLINK (RRID:SCR_009397) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/skat/

Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software)

Proper citation: SKAT (RRID:SCR_009396) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/software/simwalk

Software programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method. (entry from Genetic Analysis Software)

Proper citation: SIMWALK (RRID:SCR_009393) Copy   

•   Source: SciCrunch Registry

http://www.stat.osu.edu/~statgen/SOFTWARE/START/

Software application that finds starting points for MCMC analysis performed on large, complex pedigrees and polymorphic markers. (entry from Genetic Analysis Software)

Proper citation: START (RRID:SCR_009394) Copy   

•   Source: SciCrunch Registry

http://www.chg.duke.edu/research/simla30.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Simulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

Proper citation: SIMULA (RRID:SCR_009390) Copy   

•   Source: SciCrunch Registry

http://magnet.c2b2.columbia.edu/mutagenesys/

Software application that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: HapMap, whole-genome marker correlation data, and OMIM database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. (entry from Genetic Analysis Software)

Proper citation: MUTAGENESYS (RRID:SCR_009309) Copy   

•   Source: SciCrunch Registry

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER/OUTBRED (RRID:SCR_009306) Copy   

•   Source: SciCrunch Registry

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

Software program that selects a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. (entry from Genetic Analysis Software)

Proper citation: MULTIPOPTAGSELECT (RRID:SCR_009307) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/multidiseq/

A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software)

Proper citation: MULTIDISEQ (RRID:SCR_009304) Copy   

•   Source: SciCrunch Registry

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER (RRID:SCR_009305) Copy   

•   Source: SciCrunch Registry

http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm

A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software)

Proper citation: MPDA (RRID:SCR_009303) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.org/simped/

Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software)

Proper citation: SIMPED (RRID:SCR_009388) Copy   

•   Source: SciCrunch Registry

http://www.flintbox.com/public/project/500/

Software application to generate visual patterns that can be easily interpreted as a single specific Single Nucleotide Polymorphism (SNP) genotype, based on reiterative pattern recognition from validated SNP data (entry from Genetic Analysis Software)

Proper citation: SNP CHART (RRID:SCR_009386) Copy   

•   Source: SciCrunch Registry

http://www.gohad.uwa.edu.au/software/simhap

Software application providing a comprehensive modelling framework and a multiple-imputation approach to haplotypic analysis of population-based data. It uses biallelic SNP genotype data to impute haplotype frequencies at the individual level. SimHap also tests for haplotype associations with outcomes of interest while incorporating the uncertainty around inferred haplotypes into the modelling procedure. SimHap allows epidemiological (ie, non-genetic) and both single SNP and haplotype association analyses of quantitative Normal, binary, longitudinal and right-censored outcomes under a range of genetic models. SimHap can accommodate large data sets, and can model genetic and environmental effects, including complex haplotype:environment interactions. SimHap features cross-platform functionality via Java, and a sophisticated graphical user interface (GUI). SimHap will also perform association analysis on more simple epidemiological models, with or without the inclusion of genetic covariates. (entry from Genetic Analysis Software)

Proper citation: SIMHAP (RRID:SCR_009384) Copy   

•   Source: SciCrunch Registry

https://genepi.qimr.edu.au/staff/davidD/#sib-pair

Software program that performs a number of simple analyses of family data that tend to be nonparametric or robust in nature, includes IBD and IBS based APM, Haseman-Elston sib pair, TDT and association analyses. (entry from Genetic Analysis Software)

Proper citation: SIB-PAIR (RRID:SCR_009382) Copy   

•   Source: SciCrunch Registry