Tools   Select Another Resource Report Type

https://github.com/ABCD-STUDY/FIONASITE

Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.

Proper citation: FIONASITE (RRID:SCR_016012) Copy   

•   Source: SciCrunch Registry

http://fastml.tau.ac.il/

Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.

Proper citation: Fastml (RRID:SCR_016092) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/gubbins/

Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gubbins (RRID:SCR_016131) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/enroll

Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study.

Proper citation: enroll (RRID:SCR_016011) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nsegata/graphlan/wiki/Home

Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GraPhlAn (RRID:SCR_016130) Copy   

•   Source: SciCrunch Registry

http://standage.github.io/AEGeAn

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

Proper citation: Aegean (RRID:SCR_015965) Copy   

•   Source: SciCrunch Registry

http://www.aevol.fr/

Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

Proper citation: Aevol (RRID:SCR_015966) Copy   

•   Source: SciCrunch Registry

https://github.com/EvolBioInf/andi

Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

Proper citation: andi (RRID:SCR_015971) Copy   

•   Source: SciCrunch Registry

https://bioinf.eva.mpg.de/anfo/

Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.

Proper citation: Anfo (RRID:SCR_015972) Copy   

•   Source: SciCrunch Registry

https://github.com/dmgroppe/Mass_Univariate_ERP_Toolbox

Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests.

Proper citation: Mass Univariate ERP Toolbox (RRID:SCR_016108) Copy   

•   Source: SciCrunch Registry

http://ielvis.pbworks.com/w/page/116347253/FrontPage

Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.

Proper citation: iELVis (RRID:SCR_016109) Copy   

•   Source: SciCrunch Registry

http://www.zucic.org/garlic/

Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.

Proper citation: Garlic (RRID:SCR_016118) Copy   

•   Source: SciCrunch Registry

http://disulfind.dsi.unifi.it/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

Proper citation: DISULFIND (RRID:SCR_016072) Copy   

•   Source: SciCrunch Registry

https://github.com/boutiques/boutiques/

Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.

Proper citation: Boutiques (RRID:SCR_016073) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/vboza/deepnano

Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.

Proper citation: DeepNano (RRID:SCR_016070) Copy   

•   Source: SciCrunch Registry

http://www.statsmodels.org/

Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html

Proper citation: statsmodel (RRID:SCR_016074) Copy   

•   Source: SciCrunch Registry

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

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

Proper citation: Dotter (RRID:SCR_016080) Copy   

•   Source: SciCrunch Registry

http://bids.neuroimaging.io

Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.

Proper citation: Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/FALCON

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

Proper citation: Falcon (RRID:SCR_016089) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/geocoding

Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.

Proper citation: geocoding (RRID:SCR_016007) Copy   

•   Source: SciCrunch Registry