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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/biod/sambamba

Software tool to filter SAM file for soft and hard clipped alignments

Proper citation: samclip (RRID:SCR_024330) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/seqwish

Software tool for alignment to variation graph inducer.

Proper citation: seqwish (RRID:SCR_024332) Copy   

•   Source: SciCrunch Registry

https://github.com/cbrnr/sigviewer

Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.

Proper citation: sigviewer (RRID:SCR_024340) Copy   

•   Source: SciCrunch Registry

http://sitplus.crea-si.com/index/index.html

Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.

Proper citation: sitplus (RRID:SCR_024344) Copy   

•   Source: SciCrunch Registry

http://tacg.sourceforge.net/

Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.

Proper citation: tacg (RRID:SCR_024374) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/VelvetOptimiser/

Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.

Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy   

•   Source: SciCrunch Registry

http://visit.llnl.gov/

Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.

Proper citation: VisIt (RRID:SCR_024370) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/

Software tool to correct sequencing errors in single pass reads for de novo assembly.

Proper citation: sprai (RRID:SCR_024353) Copy   

•   Source: SciCrunch Registry

https://github.com/streamlit/streamlit

Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.

Proper citation: streamlit (RRID:SCR_024354) Copy   

•   Source: SciCrunch Registry

http://decgpu.sourceforge.net/homepage.htm

Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.

Proper citation: DecGPU (RRID:SCR_000585) Copy   

•   Source: SciCrunch Registry

https://cme.h-its.org/exelixis/web/software/sweed/

Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.

Proper citation: sweed (RRID:SCR_024357) Copy   

•   Source: SciCrunch Registry

https://github.com/magnusmanske/snpomatic

Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,

Proper citation: snpomatic (RRID:SCR_024348) Copy   

•   Source: SciCrunch Registry

http://www.workrave.org/

Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.

Proper citation: Workrave (RRID:SCR_024364) Copy   

•   Source: SciCrunch Registry

http://xmedcon.sourceforge.net/

Open source software toolkit for medical image conversion.

Proper citation: XMedCon (RRID:SCR_024366) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: VMD (RRID:SCR_024368) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry