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Software application that implements the PAC (Products of Approximate Conditional) model for estimating recombination rate (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 14 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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Software application (entry from Genetic Analysis Software)

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Software platform that is based on real haplotype data from the HapMap ENCODE project that can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users. (entry from Genetic Analysis Software)

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Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software)

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Software application for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions. (entry from Genetic Analysis Software)

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Software application (entry from Genetic Analysis Software)

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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)

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Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)

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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)

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

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

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

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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)

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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)

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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)

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Software application (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

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)

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Software application (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous