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http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/

Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)

Proper citation: MDBLOCKS (RRID:SCR_009280) Copy   

•   Source: SciCrunch Registry

http://hgc.sph.uth.tmc.edu (not available yet)

Software program for determining biological relatedness between individuals based on allele sharing at microsatellite loci (entry from Genetic Analysis Software)

Proper citation: RELTYPE (RRID:SCR_009359) Copy   

•   Source: SciCrunch Registry

http://www.biostat.jhsph.edu/~kbroman/software/

Software program for verifying the relationships between all pairs of individuals in a linkage study, by use of (autosomal) genome scan data, with allowance for the presence of genotyping errors. (entry from Genetic Analysis Software)

Proper citation: RELCHECK (RRID:SCR_009357) Copy   

•   Source: SciCrunch Registry

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

Software program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample. (entry from Genetic Analysis Software)

Proper citation: RELPAIR (RRID:SCR_009358) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. The distribution contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values. (entry from Genetic Analysis Software)

Proper citation: RC-TDT (RRID:SCR_009353) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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://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