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http://www.cs.cmu.edu/~durand/Notung/

Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses.

Proper citation: NOTUNG (RRID:SCR_024484) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=CMplot

Software drawing R package designed for Manhattan plot of genomic analysis.

Proper citation: CMplot (RRID:SCR_024514) Copy   

•   Source: SciCrunch Registry

https://github.com/PoisonAlien/Maftools

Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files.

Proper citation: maftools (RRID:SCR_024519) 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

http://www.gpower.hhu.de/

Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses.

Proper citation: G*Power (RRID:SCR_013726) Copy   

•   Source: SciCrunch Registry

http://endnote.com

A software application which helps users build a bibliography as they write formatted papers, manuscripts and other research-rich documents. Users can search multiple databases and collect PDFs as references for papers, then organize them within EndNote. Bibliographies and citations can be compiled within Microsoft Word using built-in tools. Papers are stored within an EndNote library and can be shared with colleagues.

Proper citation: EndNote (RRID:SCR_014001) Copy   

•   Source: SciCrunch Registry

http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

https://www.flowjo.com/solutions/flowjo

Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

Proper citation: FlowJo (RRID:SCR_008520) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/

Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.

Proper citation: EMBOSS (RRID:SCR_008493) Copy   

•   Source: SciCrunch Registry

http://www.project-redcap.org/

Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

Proper citation: REDCap (RRID:SCR_003445) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/sramp/

Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.

Proper citation: SRAMP (RRID:SCR_024500) Copy   

•   Source: SciCrunch Registry

http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi

Web server predict secondary structures of single stranded RNA or DNA sequences.

Proper citation: RNAfold (RRID:SCR_024427) Copy   

•   Source: SciCrunch Registry

https://nano-measurer.software.informer.com/

Software tool to process micrograph images for particle size.

Proper citation: Nano Measurer (RRID:SCR_024493) Copy   

•   Source: SciCrunch Registry