Tools   Select Another Resource Report Type

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://info.med.yale.edu/genetics/kkidd/programs.html

A simple software program for graphical presentation of haplotype block structures, tagSNP selection and SNP variation. (entry from Genetic Analysis Software)

Proper citation: HAPLOT (RRID:SCR_009228) 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://bioinfo.cs.technion.ac.il/haploblock/

Software package which provides an integrated approach to haplotype block identification, haplotype resolution and linkage disequilibrium mapping, suitable for high-density phased or unphased SNP data. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCK (RRID:SCR_009223) Copy   

•   Source: SciCrunch Registry
  

http://snp.bumc.bu.edu/modules.php?name=HaploBuild

Software application for constructing and testing haplotypes for SNPs in close physical proximity to one another but which are not necessarily contiguous. Furthermore, the number of SNPs contained in the haplotype is not restricted, thereby permitting the evaluation of complex haplotype structures. The analysis of large amounts of SNP data creates difficulties for the analysis of haplotypes and their association to traits of interest. Commonly fairly simple methods, such as two- or three-SNP sliding windows are used to create haplotypes across large regions, but these may be of limited value when adjacent SNPs are in strong LD and provide redundant information. This program alleviates these difficulties. (entry from Genetic Analysis Software)

Proper citation: HAPLOBUILD (RRID:SCR_009224) 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.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html

Software application that simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region. The disease model is specified through the choice of a single SNP as the disease causing variant together with the relative risks of the genotypes at the disease SNP. The program is designed to work with publically available files that contain the haplotypes estimated as part of the HapMap project and the estimated fine-scale recombination map derived from that data. Hapgen is computationally tractable. On a modern desktop HAPGEN can simulate several thousand case and control data on a whole chromosome at Hapmap Phase 2 marker density within minutes. This program has been used to assess the power of several different commercially available genotyping chips, in the design stage of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) and for evaluating the power of different methods for detecting association in genome-wide studies. (entry from Genetic Analysis Software)

Proper citation: HAPGEN (RRID:SCR_009221) Copy   

•   Source: SciCrunch Registry
  

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

Software application (entry from Genetic Analysis Software)

Proper citation: HAPINFERX (RRID:SCR_009222) 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://www-hto.usc.edu/msms/HapBlock/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK (RRID:SCR_009220) 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://gaow.github.io/genetic-analysis-software/l-1.html#loginserm_estihaplo

Software application (entry from Genetic Analysis Software)

Proper citation: LOGINSERM ESTIHAPLO (RRID:SCR_009258) Copy   

•   Source: SciCrunch Registry
  

http://compgen.rutgers.edu/multimap/

Software application for conversion of LINKAGE format data files to CRI-MAP format (entry from Genetic Analysis Software)

Proper citation: LNKTOCRI (RRID:SCR_009256) 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
  

http://www.ktl.fi/molbio/software/linkbase/index.html

An easy and practical database-program made for researchers who want to connect the genotype data produced by automatic sequencers ( ABI Prism 377 (Perkin Elmer) and ALF (Pharmacia) ) to linkage and sib-pair programs. (entry from Genetic Analysis Software)

Proper citation: LINKBASE (RRID:SCR_009254) Copy   

•   Source: SciCrunch Registry
  

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

Software application (entry from Genetic Analysis Software)

Proper citation: LIPED (RRID:SCR_009255) 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
  

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://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
  

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