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http://www.broadinstitute.org/mammals/haploreg/haploreg.php

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Proper citation: HaploReg (RRID:SCR_006796) Copy   

•   Source: SciCrunch Registry

http://services.bio.ifi.lmu.de/ProSAS

This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.

Proper citation: ProSAS (RRID:SCR_007876) Copy   

•   Source: SciCrunch Registry

http://www.blender.org/

Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects.

Proper citation: Blender (RRID:SCR_008606) Copy   

•   Source: SciCrunch Registry

http://scholar.google.com/

Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources

Proper citation: Google Scholar (RRID:SCR_008878) Copy   

•   Source: SciCrunch Registry

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Tool to search translated nucleotide databases using a protein query.

Proper citation: TBLASTN (RRID:SCR_011822) Copy   

•   Source: SciCrunch Registry

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry

https://www.webofscience.com/wos/woscc/advanced-search

Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.

Proper citation: Web of Science (RRID:SCR_022706) Copy   

•   Source: SciCrunch Registry

http://www.biogazelle.com/qbaseplus

Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.

Proper citation: qBasePLUS (RRID:SCR_003370) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

http://www.scipy.org/

A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.

Proper citation: SciPy (RRID:SCR_008058) Copy   

•   Source: SciCrunch Registry

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry

http://www-genepi.med.utah.edu/Genie/

Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENIE (RRID:SCR_009197) Copy   

•   Source: SciCrunch Registry

http://www.molecular-haplotype.org/profiler/profiler_intro.htm

A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PROFILER (RRID:SCR_009339) Copy   

•   Source: SciCrunch Registry

http://www.adobe.com/products/illustrator.html

Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile.

Proper citation: Adobe Illustrator (RRID:SCR_010279) Copy   

•   Source: SciCrunch Registry

http://www.maizegenetics.net/tassel

Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)

Proper citation: TASSEL (RRID:SCR_012837) Copy   

•   Source: SciCrunch Registry