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

Software application (entry from Genetic Analysis Software)

Proper citation: UNKNOWN (RRID:SCR_009423) Copy   

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http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software)

Proper citation: TFPGA (RRID:SCR_009421) Copy   

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http://www.stat.ohio-state.edu/~statgen/SOFTWARE/SIMPLE/

Software application that calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation. (entry from Genetic Analysis Software)

Proper citation: SIMPLE (RRID:SCR_009389) Copy   

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http://csg.sph.umich.edu/boehnke/simlink.php

Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)

Proper citation: SIMLINK (RRID:SCR_009387) Copy   

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http://dmpi.duke.edu/simla-simulation-software-version-32

SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software)

Proper citation: SIMLA (RRID:SCR_009385) Copy   

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http://faculty.washington.edu/browning/presto/presto.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)

Proper citation: ENDOG (RRID:SCR_013289) Copy   

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http://www.brainbank.nl

A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.

Proper citation: Netherlands Brain Bank (RRID:SCR_013841) Copy   

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http://www.openbioinformatics.org/gengen/

A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

Proper citation: GenGen (RRID:SCR_013447) Copy   

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http://hadoop.apache.org/

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

Proper citation: Apache Hadoop (RRID:SCR_011879) Copy   

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http://faculty.washington.edu/browning/beaglecall/beaglecall.html

Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)

Proper citation: BEAGLECALL (RRID:SCR_013301) Copy   

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http://dlin.web.unc.edu/software/spreg-2/

Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)

Proper citation: SPREG (RRID:SCR_013261) Copy   

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http://biomath.med.uth.gr

Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)

Proper citation: HEGESMA (RRID:SCR_013304) Copy   

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http://www.pypop.org/

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

Proper citation: PyPop (RRID:SCR_013425) Copy   

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http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

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http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

Proper citation: ANTMAP (RRID:SCR_013426) Copy   

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http://www.danielsoper.com/statcalc3/

A set of many statistics calculators, including a confidence interval calculator.

Proper citation: Statistics Calculator (RRID:SCR_013827) Copy   

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http://www.gridqtl.org.uk/

Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)

Proper citation: GRIDQTL (RRID:SCR_013397) Copy   

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http://www.tcd.ie/IMM/trinity-biobank/index.php

The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).

Proper citation: Trinity Biobank (RRID:SCR_013279) Copy   

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http://www.cns.atr.jp/dni/en/downloads/brain-decoder-toolbox/

Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent.

Proper citation: Brain Decoder Toolbox (RRID:SCR_013150) Copy   

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https://plant-breeding.uni-hohenheim.de/software.html#jfmulticontent_c110647-2

Software application (entry from Genetic Analysis Software)

Proper citation: PLABQTL (RRID:SCR_012789) Copy   

•   Source: SciCrunch Registry