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http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry

http://www.brain-map.org

Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.

Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy   

•   Source: SciCrunch Registry

http://hdbase.org/cgi-bin/welcome.cgi

A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models

Proper citation: HDBase (RRID:SCR_007132) Copy   

•   Source: SciCrunch Registry

http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software)

Proper citation: HWESTRATA (RRID:SCR_001097) Copy   

•   Source: SciCrunch Registry

http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/

Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPSCOPE (RRID:SCR_000838) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER SAD (RRID:SCR_000831) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/comds

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)

Proper citation: COMDS (RRID:SCR_000832) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/GAS2/

Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software)

Proper citation: GAS2 (RRID:SCR_001126) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)

Proper citation: CHAPLIN (RRID:SCR_000833) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimap.shtml

Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

Proper citation: CRIMAP (RRID:SCR_000834) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)

Proper citation: EQTL EXPLORER (RRID:SCR_001123) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/targetgene/

MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7

Proper citation: TARGETgene (RRID:SCR_001392) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beagle/beagle.html

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

https://www.apbenson.com/cyrillic-downloads

Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

Proper citation: CYRILLIC (RRID:SCR_001823) Copy   

•   Source: SciCrunch Registry

http://www.math.hkbu.edu.hk/~mng/CLUSTAG/CLUSTAG.html

Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.

Proper citation: CLUSTAG (RRID:SCR_001816) Copy   

•   Source: SciCrunch Registry

http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDIGREE-VISUALIZER (RRID:SCR_000842) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/haplotyping.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDPHASE (RRID:SCR_000843) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry