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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software application that can be used for the ordering of loci on genetic linkage maps. The method is based on minimisation of the total number of recombination events. Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Data files are .LOC JoinMap format. Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. 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

Software program that computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.

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• 14 years ago - by Anonymous

Software application (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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that calculates likelihood on pedigrees (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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. GenePool supports genotyping platforms from Affymetrix and Illumina.

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• 14 years ago - by Anonymous

Software application for EM algorithm estimations of SNP haplotypes (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software application that can (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

Software application for detecting recent effective population size reductions from allele data frequencies (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

Software application for semiparametric family-based association (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.

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• 14 years ago - by Anonymous

Software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. (entry from Genetic Analysis Software). QTLNetwork-2.0 for mapping quantitative trait loci (QTL) with epistatic effects and QE interaction effects in DH, RI, BC, F2, IF2 and BxFy populations, and for graphical presentation of QTL mapping results.

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• 14 years ago - by Anonymous