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http://pig.ag.uq.edu.au/qu-gene/ (not available)

Software package for quantitative analysis of genetic models (entry from Genetic Analysis Software)

Proper citation: QU-GENE (RRID:SCR_009351) Copy   

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http://www.bioinf.mdc-berlin.de/projects/hap/

Haplotype estimation service available in two variants: one for genetic data from unrelated probands (e.g., case/control studies) and one for core family data (entry from Genetic Analysis Software)

Proper citation: HAPLOTYPE ESTIMATION (RRID:SCR_009231) Copy   

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http://www.riscalw.uni-hd.de

Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account. (entry from Genetic Analysis Software)

Proper citation: RISCALW (RRID:SCR_009352) Copy   

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http://hg-wen.uchicago.edu/selection/haplotter.htm

A web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. It can be used as a resource to examine various population genetic measures in a genomic region. Measures that are currently displayed include iHS (a statistic developed to detect recent positive selection), Fay and Wu''s H, Tajima''s D and Fst. (entry from Genetic Analysis Software)

Proper citation: HAPLOTTER (RRID:SCR_009229) Copy   

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http://mayoresearch.mayo.edu/mayo/research/biostat/schaid.cfm

A suite of routines for the analysis of indirectly measured haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPLO.STAT (RRID:SCR_009227) Copy   

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http://haplopool.icsi.berkeley.edu/haplopool/

Software program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4. (entry from Genetic Analysis Software)

Proper citation: HAPLOPOOL (RRID:SCR_009225) Copy   

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

A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. (entry from Genetic Analysis Software)

Proper citation: PSEUDOMARKER.M (RRID:SCR_009346) Copy   

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http://bioinformatics.med.yale.edu/group/software.html

Software application for haplotype reconstruction in general pedigree without recombination (entry from Genetic Analysis Software)

Proper citation: HAPLORE (RRID:SCR_009226) Copy   

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http://www.sph.umich.edu/csg/abecasis/pseudo/download

Software application that estimates genomewide empirical p-values for Kong and Cox tests of linkage using the replicate pool method, which for many data sets, improves upon the computational efficiency of conventional gene-dropping methods by several orders of magnitude. This allows Pseudo to handle data sets with large families and makes it particularly applicable to those situations where p-value estimation by standard methods is computationally prohibitive. Pseudo also estimates variance for reported p-values, produces graphical and text summaries of results, and is able to assess significance of multiple correlated outcomes. Pseudo is designed to work with the Merlin package and includes utilities for generating input files from standard Merlin output. (entry from Genetic Analysis Software)

Proper citation: PSEUDO (RRID:SCR_009344) Copy   

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http://support.sas.com/documentation/onlinedoc/genetics/

Software application for summarizing marker properties (allele & genotype frequencies, tests for Hardy-Weinberg equilibrium, measures of marker informativeness), examining marker-marker relationships (tests and measures of linkage disequilibrium, and haplotype frequency estimation), and exploring marker-trait associations using case-control or family-based tests (entry from Genetic Analysis Software)

Proper citation: SAS/GENETICS (RRID:SCR_009343) Copy   

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http://www.maths.lancs.ac.uk/~fearnhea/Hotspot/

Software program that analyzes sequence data. It obtains an approximation to the likelihood of a summary of the data (as such it can be thought of as a marginal likelihood approach). It does not use all the information in the data, but computationally it can be substantially more efficient than the full-likelihood methods (and hence able to analyze larger data sets). (entry from Genetic Analysis Software)

Proper citation: SEQUENCE LD/SEQUENCE LDHOT (RRID:SCR_009379) Copy   

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http://www.bioinf.mdc-berlin.de/~rohde/

Software program using loss of heterozygosity data to enhance the power to detect linkage in cancer families. (entry from Genetic Analysis Software)

Proper citation: LOH-LINKAGE (RRID:SCR_009259) Copy   

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https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics. (entry from Genetic Analysis Software)

Proper citation: SDMINP (RRID:SCR_009377) Copy   

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http://genome.sph.umich.edu/wiki/LocusZoom

Software application designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about How did you make the figures in your talk? or How did you make the figures for your GWAS paper? (entry from Genetic Analysis Software)

Proper citation: LOCUSZOOM (RRID:SCR_009257) Copy   

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

An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software)

Proper citation: R/SNP.PLOTTER (RRID:SCR_009376) Copy   

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http://evolution.genetics.washington.edu/lamarc/lamarc_prog.html

Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software)

Proper citation: LAMARC (RRID:SCR_009252) Copy   

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https://epi.mdanderson.org/~xzhou/Software/Linkage_imprinting/

Software application that is a parametric model-based approach to analyzing pedigree data for genomic imprinting. They have modified widely used LINKAGE program to incorporate imprinting. In addition, the LINKAGE-IMPRINT program allows for the use of sex-specific recombination in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. (entry from Genetic Analysis Software)

Proper citation: LINKAGE-IMPRINT (RRID:SCR_009253) Copy   

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http://people.virginia.edu/~wc9c/KING/

Software toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) for applications such as family relationship inference and population structure identification (entry from Genetic Analysis Software)

Proper citation: KING (RRID:SCR_009251) Copy   

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

An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software)

Proper citation: R/METASIM (RRID:SCR_009370) Copy   

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http://www.genepi.org.au/jlin

Software application designed for customizable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D'' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q. (entry from Genetic Analysis Software)

Proper citation: JLIN (RRID:SCR_009247) Copy   

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