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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   

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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://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://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   

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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   

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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   

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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   

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http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

•   Source: SciCrunch Registry

http://www.aps.uoguelph.ca/~msargol/qmsim/

Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)

Proper citation: QMSIM (RRID:SCR_013123) Copy   

•   Source: SciCrunch Registry

https://imdevsoftware.wordpress.com/imdev/

A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.

Proper citation: imDEV (RRID:SCR_014674) Copy   

•   Source: SciCrunch Registry

http://prospector.ucsf.edu

A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.

Proper citation: Protein Prospector (RRID:SCR_014558) Copy   

•   Source: SciCrunch Registry

http://web.cmb.usc.edu/people/alber/Software/tomominer/

Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.

Proper citation: TomoMiner (RRID:SCR_015045) Copy   

•   Source: SciCrunch Registry

http://www.microbesonline.org/fasttree/

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

Proper citation: FastTree (RRID:SCR_015501) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/lme4/index.html

Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."

Proper citation: lme4 (RRID:SCR_015654) Copy   

•   Source: SciCrunch Registry

http://metap.helmholtz-muenchen.de/metap2/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetaP (RRID:SCR_014686) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/go2msig/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists.
Gene set collections can be automatically created for wide variety of species.

Proper citation: GO2MSIG (RRID:SCR_018359) Copy   

•   Source: SciCrunch Registry