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

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)

Proper citation: ASSOCIATIONVIEWER (RRID:SCR_009063) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that uses multilocus genotypic data to allocate individuals to their most likely source population.

Proper citation: WHICHRUN (RRID:SCR_009064) Copy   

•   Source: SciCrunch Registry

http://www.mapmanager.org/mmQTX.html

A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals. A completely rewritten cross-platform version of Map Manager QT with enhanced analysis functions. (entry from Genetic Analysis Software)

Proper citation: MAP MANAGER QTX (RRID:SCR_009061) Copy   

•   Source: SciCrunch Registry

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

Software tool for construction of genetic linkage maps and analyzing Mendelian phenotypes. (entry from Genetic Analysis Software)

Proper citation: G-MENDEL (RRID:SCR_009062) Copy   

•   Source: SciCrunch Registry

http://fmph.ucsd.edu/faculty/cberry/bqtl/

Software application for the mapping of genetic traits from line crosses and recombinant inbred lines. It performs (1) maximum likelihood estimation of multi-gene models; (2) Bayesian estimation of multi-gene models via Laplace Approximations; and (3) interval mapping and composite interval mapping of genetic loci (entry from Genetic Analysis Software)

Proper citation: BQTL (RRID:SCR_009137) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/d-1.html#dnabaser

Software tool for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DNABASER (RRID:SCR_009138) Copy   

•   Source: SciCrunch Registry

http://wwwcsif.cs.ucdavis.edu/~gusfield/bpph.html

Software application for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. (entry from Genetic Analysis Software)

Proper citation: BPPH (RRID:SCR_009136) Copy   

•   Source: SciCrunch Registry

http://www.cs.auc.dk/~claus/block.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that performs general pedigree analysis on a general pedigree with any number of loops. It also allows users to perform two-point linkage analysis on a general pedigree with an arbitrary number of alleles., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLOCK (RRID:SCR_009133) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/rarevariant/

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)

Proper citation: QUTIE (RRID:SCR_009098) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.forsyth.org/

Core specializes in oral microbial genomics, taxonomy, phylogenetics and the next generation sequence (NGS) data analysis with both in house and cloud high performance computational resource. In addition to supporting funded bioinformatics projects, Bioinformatics Core will also provide computational support to Forsyth and other researchers for processing, analyzing, and interpreting biological data.

Proper citation: Forsyth Institute Bioinformatics Core Facility (RRID:SCR_009783) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

http://www.cpgr.org.za

Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry.

Proper citation: University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility (RRID:SCR_017158) Copy   

•   Source: SciCrunch Registry

https://dnacore.missouri.edu/

Core research facility providing genomic services that include next generation sequencing , single cell sequencing, metagenomic, targeted amplicon sequencing, and Sanger sequencing.

Proper citation: University of Missouri-Columbia DNA Core Facility (RRID:SCR_017778) Copy   

•   Source: SciCrunch Registry

https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies

Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma.

Proper citation: Duke University Sequencing and Genomic Technologies Core Facility (RRID:SCR_017748) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/index1.html

Software application (entry from Genetic Analysis Software)

Proper citation: BLADE (RRID:SCR_009132) Copy   

•   Source: SciCrunch Registry

http://hg-wen.uchicago.edu/software.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Software application (entry from Genetic Analysis Software)

Proper citation: STEPC (RRID:SCR_009096) Copy   

•   Source: SciCrunch Registry

http://www.plantbreeding.wur.nl/UK/software_record.html

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)

Proper citation: RECORD (RRID:SCR_009097) Copy   

•   Source: SciCrunch Registry

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

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)

Proper citation: TDT-AE (RRID:SCR_009094) Copy   

•   Source: SciCrunch Registry

https://github.com/genomizer/genomizer.github.io

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A platform independent Java program for the analysis of genome wide association experiments. (entry from Genetic Analysis Software).

Proper citation: GENOMIZER (RRID:SCR_009127) Copy   

•   Source: SciCrunch Registry