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http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

Proper citation: Haploview (RRID:SCR_003076) Copy   

•   Source: SciCrunch Registry

http://www.biosciences-labs.bham.ac.uk/Kearsey/

Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software)

Proper citation: QTL CAFE (RRID:SCR_000844) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/fdudbridge/software/pelican

Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

Proper citation: PELICAN (RRID:SCR_001695) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

http://genomics.med.upenn.edu/spielman/TDT.htm

Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)

Proper citation: TDT/S-TDT (RRID:SCR_005548) Copy   

•   Source: SciCrunch Registry

https://varscan.sourceforge.net/

Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software).

Proper citation: VarScan (RRID:SCR_006849) Copy   

•   Source: SciCrunch Registry

https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

•   Source: SciCrunch Registry

http://www.jenti.org

An efficient tool for mining complex inbred genealogies that identify clusters of individuals sharing the same expected amount of relatedness is described. Additionally it allows for the reconstruction of sub-pedigrees suitable for genetic mapping in a systematic way. (entry from Genetic Analysis Software)

Proper citation: JENTI (RRID:SCR_009053) Copy   

•   Source: SciCrunch Registry

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

A set of Java programs for genetic epidemiology analysis (entry from Genetic Analysis Software)

Proper citation: GENEPI.JAR (RRID:SCR_008782) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/u/prastas/haplovisual/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOVISUAL (RRID:SCR_009073) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/SNPHarvester.html

Software tool for detecting epistatic interactions in genome-wide association studies (entry from Genetic Analysis Software)

Proper citation: SNPHARVESTER (RRID:SCR_008536) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: IGG (RRID:SCR_009114) Copy   

•   Source: SciCrunch Registry

http://embio.yonsei.ac.kr/haplowser/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOWSER (RRID:SCR_009095) Copy   

•   Source: SciCrunch Registry

http://www.genoproof.com or http://qualitype.de/genoproof/

Software package for the analysis of multiplex PCR kits within the scope of paternity testing, kinship cases and population studies. GenoProof offers: (1) probably the most extensive existing population database for all supported markers of more than 50 ethnic groups, (2) individually configurable quality assurance options, (3) complex concept of user rights in order to guarantee data security, (4) languages German and English (entry from Genetic Analysis Software)

Proper citation: GENOPROOF (RRID:SCR_009204) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/genevar/

A database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies. Genevar allows researchers to investigate eQTL (expression quantitative trait loci) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the internet via web services protocols. (entry from Genetic Analysis Software)

Proper citation: GENEVAR (RRID:SCR_009201) Copy   

•   Source: SciCrunch Registry

http://carlit.toulouse.inra.fr/MCQTL/

Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)

Proper citation: MCQTL (RRID:SCR_009285) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/staff/churchill/labsite/software/Jqtl/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A Java GUI for the popular QTL data analysis software R/QTL that provides a flexible and powerful working environment for users to perform a variety of tasks. (entry from Genetic Analysis Software)

Proper citation: J/QTL (RRID:SCR_009250) Copy   

•   Source: SciCrunch Registry

http://balance.med.utah.edu/wiki/index.php/JPSGCS

Software application to address problems in statistical genetics; however, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models. (entry from Genetic Analysis Software)

Proper citation: JPSGCS (RRID:SCR_009249) 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