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http://www.jurgott.org/linkage/sumstat.html

Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software)

Proper citation: SUMSTAT (RRID:SCR_009416) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software.

Proper citation: SUP (RRID:SCR_009417) Copy   

•   Source: SciCrunch Registry

http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software)

Proper citation: SASGENE (RRID:SCR_013084) Copy   

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https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)

Proper citation: SNPTEST (RRID:SCR_009406) Copy   

•   Source: SciCrunch Registry

http://www.maizegenetics.net/tassel

Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)

Proper citation: TASSEL (RRID:SCR_012837) Copy   

•   Source: SciCrunch Registry

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

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

Proper citation: PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) Copy   

•   Source: SciCrunch Registry

http://genecanvas.ecgene.net/#!index.md#THESIAS:_testing_haplotype_effects_in_association_studies

Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software)

Proper citation: THESIAS (RRID:SCR_013449) Copy   

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http://www.stat.washington.edu/thompson/Genepi/Eclipse.shtml

A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software)

Proper citation: ECLIPSE (RRID:SCR_013130) Copy   

•   Source: SciCrunch Registry

http://www.dynacom.co.jp/u-tokyo.ac.jp/snphitlink/

Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)

Proper citation: SNP HITLINK (RRID:SCR_013340) Copy   

•   Source: SciCrunch Registry

https://github.com/telatin/covtobed

Software tool to generate BED coverage tracks from BAM files.

Proper citation: covtobed (RRID:SCR_023998) Copy   

•   Source: SciCrunch Registry

http://bioinfo.unl.edu/gramalign.php

Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.

Proper citation: GramAlign (RRID:SCR_024032) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj

Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.

Proper citation: BioMAJ (RRID:SCR_023983) Copy   

•   Source: SciCrunch Registry

https://www.gnumed.de/documentation/

Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.

Proper citation: GNUmed (RRID:SCR_024029) Copy   

•   Source: SciCrunch Registry

http://ruby.chemie.uni-freiburg.de/~martin/chemtool/

Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.

Proper citation: Chemtool (RRID:SCR_023992) Copy   

•   Source: SciCrunch Registry

http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/

Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.

Proper citation: ChromImpute (RRID:SCR_023990) Copy   

•   Source: SciCrunch Registry

https://entangle-photo.org/

Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.

Proper citation: Entangle (RRID:SCR_024015) Copy   

•   Source: SciCrunch Registry

https://github.com/fccoelho/epigrass

Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.

Proper citation: Epigrass (RRID:SCR_024016) Copy   

•   Source: SciCrunch Registry

https://github.com/jnktsj/DNApi/

Software de novo adapter prediction algorithm for small RNA sequencing data.

Proper citation: DNApi (RRID:SCR_024009) Copy   

•   Source: SciCrunch Registry

https://www.teuniz.net/edfbrowser/

Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.

Proper citation: EDFbrowser (RRID:SCR_024021) Copy   

•   Source: SciCrunch Registry

http://assemblytics.com/

Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.

Proper citation: Assemblytics (RRID:SCR_023967) Copy   

•   Source: SciCrunch Registry