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http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LAMBDAA (RRID:SCR_001128) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LDMET (RRID:SCR_001127) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

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

Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)

Proper citation: POLYMUTT (RRID:SCR_002051) Copy   

•   Source: SciCrunch Registry

https://hsph.harvard.edu/research/price-lab/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/birdsuite/birdsuite

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

Proper citation: BIRDSUITE (RRID:SCR_001794) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/dindel

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Proper citation: DINDEL (RRID:SCR_001827) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

http://ccb.loni.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging.

Proper citation: Center for Computational Biology at UCLA (RRID:SCR_000334) Copy   

•   Source: SciCrunch Registry

http://www.semel.ucla.edu/creativity/

The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits the most advanced techniques for genetic manipulation and basic neurobiological research to be applied in close collaboration with human studies that converge on the same core cognitive processes. Our integrated research program aims to reveal the genetic architecture and fundamental brain mechanisms underlying creative cognition. The work holds enormous promise for both enhancing healthy cognitive performance and designing new treatments for diverse cognitive disorders. Sponsors: The Tennenbaum Center for the Biology of Creativity was inspired by the vision and generosity of Michael Tennenbaum.

Proper citation: Tennenbaum Center for the Biology of Creativity (RRID:SCR_000668) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAP (RRID:SCR_000689) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/pseudomarker/

A linkage analysis software for joint linkage and/or linkage disequilibrium analysis. PSEUDOMARKER can analyze different data structures jointly such as cases-controls, trios, sib-pairs, sib-ships, and extended families. (entry from Genetic Analysis Software)

Proper citation: PSEUDOMARKER (RRID:SCR_009345) Copy   

•   Source: SciCrunch Registry

http://www.urmc.rochester.edu/smd/biostat/Projects/Help/PC/Software_Listings.htm

Software application for partition of single generation into sibling groups (entry from Genetic Analysis Software)

Proper citation: PRT (RRID:SCR_009340) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/psat/

Software application (entry from Genetic Analysis Software)

Proper citation: PSAT (RRID:SCR_009341) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~spencer/SelSim/

Software program which can simulate population genetic data in which a single site has experienced natural selection. When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. (entry from Genetic Analysis Software)

Proper citation: SELSIM (RRID:SCR_009378) Copy   

•   Source: SciCrunch Registry

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

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

•   Source: SciCrunch Registry

http://www.adfg.alaska.gov/index.cfm?adfg=fishinggeneconservationlab.software

Software application that estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem. (entry from Genetic Analysis Software)

Proper citation: SPAM (RRID:SCR_009407) Copy   

•   Source: SciCrunch Registry

https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)

Proper citation: SNPTEST (RRID:SCR_009406) Copy   

•   Source: SciCrunch Registry

http://www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm

Software application for multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available. (entry from Genetic Analysis Software)

Proper citation: SNPLINK (RRID:SCR_009403) Copy   

•   Source: SciCrunch Registry