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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   

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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   

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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   

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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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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://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   

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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   

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http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

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http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

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

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

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http://people.virginia.edu/~wc9c/TDTPC/Download.htm

Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Proper citation: TDT-PC (RRID:SCR_001116) Copy   

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http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

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http://www.rightfield.org.uk/

An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Proper citation: RightField (RRID:SCR_002649) Copy   

•   Source: SciCrunch Registry

http://www.altanalyze.org/

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

Proper citation: AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) Copy   

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https://sites.google.com/a/brain.org.au/ctp/

Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cortex (RRID:SCR_002467) Copy   

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https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/

A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.

Proper citation: Yabi (RRID:SCR_005359) Copy   

•   Source: SciCrunch Registry