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on page 1 showing 20 out of 541 results from 1 sources

    2DMAP

Cite this (2DMAP, RRID:SCR_009036)

URL: http://www.genlink.wustl.edu/software

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.

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    2LD

Cite this (2LD, RRID:SCR_000826)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2LD.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

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    2SNP

Cite this (2SNP, RRID:SCR_009038)

URL: https://github.com/gaow/genetic-analysis-software/blob/master/pages/2SNP.md

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.

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    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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    AGEINF

Cite this (AGEINF, RRID:SCR_009039)

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

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.

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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)

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    ALLEGRO

Cite this (ALLEGRO, RRID:SCR_009116)

URL: http://www.decode.com/software/

Resource Type: Resource, software resource, software application

Software application that is a faster version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed, can handle bigger families, up to 50 bits) (entry from Genetic Analysis Software)

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    ALLELIX

Cite this (ALLELIX, RRID:SCR_009115)

URL: http://www.allelix.net

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de)

  • 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)

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    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)

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    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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    ANALYZE

Cite this (ANALYZE, RRID:SCR_009120)

URL: http://www.helsinki.fi/~tsjuntun/linkage/analyze/

Resource Type: Resource, software resource, software application

A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software)

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    ANCESTRY

Cite this (ANCESTRY, RRID:SCR_009121)

URL: http://ciil.case.edu:3000

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides an easy to use web-based user interface to compute individual ancestry estimates using the Maximum Likelihood Estimation method. This website also allows registered users to manage genotype and marker/allele frequency files. Registration is optional.

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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)

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    APE

Cite this (APE, RRID:SCR_009122)

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

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that extends partially observed genotype data to the whole pedigree. Can be used for generating starting points for MCMC samplers and for checking that the genotype data are consistent with the pedigree structure.

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    APL-OSA

Cite this (APL-OSA, RRID:SCR_009124)

URL: http://dmpi.duke.edu/apl-osa-beta-version

Resource Type: Resource, software resource, software application

Software application that in the presence of genetic heterogeneity, can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage and the family-based association test, APL. Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time. (entry from Genetic Analysis Software)

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