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on page 1 showing 20 out of 325 results

    ACT

Cite this (ACT, RRID:SCR_009033)

URL: http://www.epigenetic.org/Linkage/act.html,

Resource Type: Resource, software resource, software application

Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software)

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    ADEGENET

Cite this (ADEGENET, RRID:SCR_000825)

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

Resource Type: Resource, software resource, software application

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

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    ADMIXMAP

Cite this (ADMIXMAP, RRID:SCR_009035)

URL: http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

Resource Type: Resource, software resource, software application

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

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    ALBERT

Cite this (ALBERT, RRID:SCR_009037)

URL: http://www.stat.washington.edu/thompson/Genepi/Albert/albert.shtml

Resource Type: Resource, software resource, software application

Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software)

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    ALLASS

Cite this (ALLASS, RRID:SCR_009040)

URL: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ALLASS

Resource Type: Resource, software resource, software application

Software application (entry from Genetic Analysis Software)

  • From Current Category

Cite this (ALOHOMORA, RRID:SCR_009117)

URL: http://gmc.mdc-berlin.de/alohomora/

Resource Type: Resource, software resource, software application

Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)

  • From Current Category

    ALP

Cite this (ALP, RRID:SCR_009118)

URL: http://www.hgu.mrc.ac.uk/Softdata/ALP/

Resource Type: Resource, software resource, software application

Microsoft Windows application designed to analyze microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer. (entry from Genetic Analysis Software)

  • From Current Category

    ALTREE

Cite this (ALTREE, RRID:SCR_007562)

URL: http://claire.bardel.free.fr/software.html

Resource Type: Resource, software resource, software application

Software application that performs these two phylogeny-based analysis: (1) it tests the association between a candidate gene and a disease; (2) it pinpoints markers (SNPs) that are putative disease susceptibility loci (entry from Genetic Analysis Software)

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    AMELIA

Cite this (AMELIA, RRID:SCR_009119)

URL: http://www.sanger.ac.uk/resources/software/amelia/

Resource Type: Resource, software resource, software application

Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)

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    ANTMAP

Cite this (ANTMAP, RRID:SCR_013426)

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

Resource Type: Resource, software resource, software application

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)

  • From Current Category

    APM

Cite this (APM, RRID:SCR_009125)

URL: http://watson.hgen.pitt.edu/register/soft_doc.html registration page at: http://watson.hgen.pitt.edu/register

Resource Type: Resource, software resource, software application

Software application (entry from Genetic Analysis Software)

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    ARIEL

Cite this (ARIEL, RRID:SCR_009126)

URL: http://www.sanger.ac.uk/resources/software/ariel/

Resource Type: Resource, software resource, software application

Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)

  • From Current Category

    ARLEQUIN

Cite this (ARLEQUIN, RRID:SCR_009051)

URL: http://cmpg.unibe.ch/software/arlequin3/

Resource Type: Resource, software resource, software application

An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)

  • From Current Category

Cite this (ASP/ASPSHARE, RRID:SCR_009128)

URL: http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/

Resource Type: Resource, software resource, software application

Software applications including ASP, a power calculator for gene mapping using a sibpair design (concordant or discordant) and ASPSHARE, which complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. (entry from Genetic Analysis Software)

  • From Current Category

    ASPEX

Cite this (ASPEX, RRID:SCR_008414)

URL: http://aspex.sourceforge.net/

Resource Type: Resource, software resource, software application

A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software)

  • From Current Category

Cite this (ASSOCIATIONVIEWER, RRID:SCR_009063)

URL: http://associationviewer.vital-it.ch/

Resource Type: Resource, software resource, software application

A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software)

  • From Current Category

    AUTOSCAN

Cite this (AUTOSCAN, RRID:SCR_013510)

URL: http://www.helsinki.fi/~tsjuntun/autoscan/

Resource Type: Resource, software resource, software application

A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)

  • From Current Category

    BAMA

Cite this (BAMA, RRID:SCR_009071)

URL: http://www.rni.helsinki.fi/~mjs/

Resource Type: Resource, software resource, software application

Software application to select a trait-associated subset of markers among many candidates. The program is based on Bayesian modeling/estimation and it suits for both quantitative and qualitative traits. It can handle bi- and multiallelic markers as well as applied in situations where part of the marker genotypes may be missing. As an output of the program, one obtains posterior estimate of number and positions of trait-associated markers. (entry from Genetic Analysis Software)

  • From Current Category

    BARS

Cite this (BARS, RRID:SCR_009123)

URL: http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

Resource Type: Resource, software resource, software application

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software)

  • From Current Category

    BAYESFST

Cite this (BAYESFST, RRID:SCR_013479)

URL: http://www.reading.ac.uk/Statistics/genetics/software.html

Resource Type: Resource, software resource, software application

Software application for Bayesian estimation of the coancestry coefficient FST (entry from Genetic Analysis Software)

  • From Current Category

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