Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: PSAT (RRID:SCR_009341) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.adfg.alaska.gov/index.cfm?adfg=fishinggeneconservationlab.software

Software application that estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem. (entry from Genetic Analysis Software)

Proper citation: SPAM (RRID:SCR_009407) Copy   

•   Source: SciCrunch Registry

https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)

Proper citation: SNPTEST (RRID:SCR_009406) Copy   

•   Source: SciCrunch Registry

http://www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm

Software application for multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available. (entry from Genetic Analysis Software)

Proper citation: SNPLINK (RRID:SCR_009403) Copy   

•   Source: SciCrunch Registry

http://orclinux.creighton.edu/snpp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.

Proper citation: SNPP (RRID:SCR_009404) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: RHMAP (RRID:SCR_009360) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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