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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://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.angelfire.com/mn2/nath/gems.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.

Proper citation: GEMS (RRID:SCR_009188) Copy   

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http://www.mybiosoftware.com/genecounting-2-2-gene-counting-haplotype-analysis.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

Proper citation: GENECOUNTING (RRID:SCR_009189) Copy   

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http://episun7.med.utah.edu/~alun/gchap/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

Proper citation: GCHAP (RRID:SCR_009186) Copy   

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http://www.epicentersoftware.com/products.php

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors. (entry from Genetic Analysis Software)

Proper citation: GAP (RRID:SCR_009183) 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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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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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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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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http://www.joinmap.nl/

Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)

Proper citation: JOINMAP (RRID:SCR_009248) Copy   

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https://mathgen.stats.ox.ac.uk/impute/impute.html

Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)

Proper citation: IMPUTE (RRID:SCR_009245) Copy   

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http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=mdrpdt

Software application (entry from Genetic Analysis Software)

Proper citation: MDR-PDT (RRID:SCR_009243) Copy   

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http://intersnp.meb.uni-bonn.de/

Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software)

Proper citation: INTERSNP (RRID:SCR_009244) Copy   

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http://www.chgb.org.cn/htSNPer/htSNPer.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software)

Proper citation: HTSNPER (RRID:SCR_009242) Copy   

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http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

•   Source: SciCrunch Registry