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http://qtl.cap.ed.ac.uk/

A web-based user-friendly package to map Quantitative Trait Loci in outbred populations. Population structures catered for are line crosses, halfsib families, nuclear families and sibpairs. Permutation tests to determine empirical significance levels and bootstrapping to estimate empirical confidence intervals of QTL locations are optional. Fixed effects/covariates can be fitted and models may include single or multiple QTL. Results are presented in tabular and graphical format. (entry from Genetic Analysis Software)

Proper citation: QTL EXPRESS (RRID:SCR_009350) Copy   

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http://watson.hgen.pitt.edu/register/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software package designed to make as many as possible of the new statistics (e.g. score statistics) widely available. The software consists of a MEGA2-like interface for data analysis preparation and a library of R routines that computes linkage statistics. QTL-ALL reads in input data, creates re-formatted output data files, calls external IBD-generation software such as MERLIN or SIMWALK2, then computes statistics using our R library, and finally produces tables and plots of statistics and p-values. This entire sequence is highly automated, requiring minimal user-intervention. The initial release of the software computes a number of newer QTL-mapping statistics, including several score statistic variants, and can handle nuclear family data, including specialty designs such as discordant and concordant (affected) pairs. (entry from Genetic Analysis Software)

Proper citation: QTL-ALL (RRID:SCR_009348) Copy   

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http://statgen.ncsu.edu/qtlcart/cartographer.html

Software program to map quantitative traits sing a map of molecular markers. (entry from Genetic Analysis Software)

Proper citation: QTL Cartographer (RRID:SCR_009349) Copy   

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

A linkage analysis software for joint linkage and/or linkage disequilibrium analysis. PSEUDOMARKER can analyze different data structures jointly such as cases-controls, trios, sib-pairs, sib-ships, and extended families. (entry from Genetic Analysis Software)

Proper citation: PSEUDOMARKER (RRID:SCR_009345) Copy   

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http://www.urmc.rochester.edu/smd/biostat/Projects/Help/PC/Software_Listings.htm

Software application for partition of single generation into sibling groups (entry from Genetic Analysis Software)

Proper citation: PRT (RRID:SCR_009340) Copy   

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http://acgt.cs.tau.ac.il/psat/

Software application (entry from Genetic Analysis Software)

Proper citation: PSAT (RRID:SCR_009341) Copy   

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http://www.well.ox.ac.uk/~spencer/SelSim/

Software program which can simulate population genetic data in which a single site has experienced natural selection. When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. (entry from Genetic Analysis Software)

Proper citation: SELSIM (RRID:SCR_009378) Copy   

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

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: R/LUCA (RRID:SCR_009369) Copy   

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http://capella.uni-kiel.de/snap/snap.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.

Proper citation: SNAP 3 (RRID:SCR_009400) Copy   

•   Source: SciCrunch Registry

http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-progs.htm

An integrated software package for genetic data analysis of both population and family data. Currently it contains functions for sample size calculations of both population-based and family-based designs, classic twin ACE/ADE/AE/CE models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates (entry from Genetic Analysis Software)

Proper citation: R/GAP (RRID:SCR_009364) Copy   

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

Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)

Proper citation: R/HAPASSOC (RRID:SCR_009365) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: RHMAP (RRID:SCR_009360) Copy   

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http://www.chg.duke.edu/software/pdt.html

Software analysis program to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets. (entry from Genetic Analysis Software)

Proper citation: PDT (RRID:SCR_009319) Copy   

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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   

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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   

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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   

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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   

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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   

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

Software application (entry from Genetic Analysis Software)

Proper citation: SLINK (RRID:SCR_009397) Copy   

•   Source: SciCrunch Registry