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

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)

Proper citation: ALOHOMORA (RRID:SCR_009117) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)

Proper citation: CASPAR (RRID:SCR_009074) Copy   

•   Source: SciCrunch Registry

http://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html#c63682

Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait.

Proper citation: genehunter-imprinting (RRID:SCR_009104) Copy   

•   Source: SciCrunch Registry

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

http://www.stat.auckland.ac.nz/~browning/ccrel/ccrel.htm

Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software)

Proper citation: CCREL (RRID:SCR_009142) Copy   

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http://genome.sph.umich.edu/wiki/ExomePicks

Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software)

Proper citation: EXOMEPICKS (RRID:SCR_009174) Copy   

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http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

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http://research.nhgri.nih.gov/ROMPrev/

Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)

Proper citation: ROMPREV (RRID:SCR_009361) Copy   

•   Source: SciCrunch Registry

http://www.unc.edu/~yunmli/MaCH-Admix/

A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix.

Proper citation: MaCH-Admix (RRID:SCR_009598) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

https://github.com/Gregor-Mendel-Institute/poolhap

Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples.

Proper citation: PoolHap (RRID:SCR_012129) Copy   

•   Source: SciCrunch Registry

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

Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)

Proper citation: SIMULATE (RRID:SCR_009391) Copy   

•   Source: SciCrunch Registry

http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take

Proper citation: SNPAAMapper (RRID:SCR_002012) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/skewer/

Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

Proper citation: skewer (RRID:SCR_001151) Copy   

•   Source: SciCrunch Registry

https://github.com/princelab/mspire-simulator

A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.

Proper citation: Mspire-Simulator (RRID:SCR_001431) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/HTqPCR.html

Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

Proper citation: HTqPCR (RRID:SCR_003375) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/NanoStringNorm/

Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

Proper citation: NanoStringNorm (RRID:SCR_003382) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/circlize/

Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

Proper citation: circlize (RRID:SCR_002141) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry