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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data management software, software application, data processing software, software resource, data analysis software | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool https://bio.tools/fastqc https://sources.debian.org/src/fastqc/ |
SCR_014583 | FastQC v0.11.5 | 2026-02-15 09:20:44 | 18745 | |||||||
|
Brain Extraction Tool Resource Report Resource Website 10+ mentions |
Brain Extraction Tool (RRID:SCR_014586) | BET2, BET | software application, image processing software, data processing software, software resource | Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces. | delete non-brain tissue from image, whole head, internal and external skull surfaces estimation, |
is listed by: SoftCite is a plug in for: FSL |
Free, Freely available | http://poc.vl-e.nl/distribution/manual/fsl-3.2/bet2/ | SCR_014586 | Brain Extraction Tool (BET), Brain Extraction Tool (BET2) | 2026-02-15 09:21:05 | 16 | |||||||
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NVivo Resource Report Resource Website 10000+ mentions |
NVivo (RRID:SCR_014802) | software application, data processing software, data analysis software, software resource | Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed. | qualitative, data analysis, software, data solution | is listed by: SoftCite | SCR_014802 | 2026-02-15 09:21:00 | 11593 | |||||||||||
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Simulink Resource Report Resource Website 100+ mentions |
Simulink (RRID:SCR_014744) | software application, simulation software, software toolkit, software resource | Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems. | matlab, block diagram, multidomain simulation, simulation software, model based design, automatic code generation | is listed by: SoftCite | Commercially available, Free trial available | SCR_014744 | 2026-02-15 09:20:45 | 364 | ||||||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | software application, data processing software, software resource, web application, data analysis software | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3 https://bio.tools/prottest https://sources.debian.org/src/prottest/ |
SCR_014628 | 2026-02-15 09:20:44 | 1981 | |||||||
|
IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | software application, sequence analysis software, data processing software, software resource, web application, data analysis software | A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence. | web application, sequence analysis, web server, territory structure, amino acid sequence, swiss prot, trembl | is listed by: SoftCite | PMID:15955779 | Available to academic users, Available for download, Commercial users must enquire | SCR_014632 | Prediction of Intrinsically Unstructured Proteins, Prediction of Intrinsically Unstructured Proteins (IUPRED) | 2026-02-15 09:20:45 | 295 | ||||||||
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FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | web application, software resource | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-02-15 09:21:06 | 139 | |||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | software application, sequence analysis software, data processing software, software resource, alignment software, image analysis software, data analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml https://github.com/BenLangmead/bowtie2 https://bio.tools/bowtie2 |
SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-02-15 09:20:59 | 1745 | |||||
|
WinWCP Resource Report Resource Website 100+ mentions |
WinWCP (RRID:SCR_014713) | software application, data processing software, software resource, data acquisition software, data analysis software | Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection. | data analysis software, whole cell, voltage, current, clamp experiments, neuron, neuroinformatics, single cell recording |
is listed by: SoftCite is affiliated with: Strathclyde Electrophysiology Suite |
Open source for academic and non-profit use, License available for purchase for commercial organizations | SCR_014713 | Windows Whole Cell Program | 2026-02-15 09:21:01 | 412 | |||||||||
|
PAUP Resource Report Resource Website 1000+ mentions |
PAUP (RRID:SCR_014931) | PAUP | software application, data visualization software, data processing software, software resource, data analysis software | Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis. | phylogenetic tree, phylogeny, evolutionary tree, molecular data, morphological data, behavioral data |
is listed by: SoftCite works with: PAML |
Free | http://people.sc.fsu.edu/~dswofford/paup_test/ | SCR_014931 | Phylogenetic Analysis Using Parsimony | 2026-02-15 09:21:03 | 2266 | |||||||
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Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | software application, data processing software, data acquisition software, software resource | Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment. | biomechanics, motion capture |
is listed by: SoftCite works with: MATLAB works with: Bodybuilder |
Available for download | https://www.vicon.com/downloads/core-software/nexus | SCR_015001 | Nexus 2, Nexus 1.8.5, Nexus 2.5.0, Nexus 2.4.0 | 2026-02-15 09:20:48 | 373 | ||||||||
|
Statgraphics Centurion Resource Report Resource Website 1+ mentions |
Statgraphics Centurion (RRID:SCR_015248) | software application, data visualization software, data processing software, software resource, data analysis software | Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers. | statistical analysis software, statistical visualization software, statistical analysis | is listed by: SoftCite | Available for download, Trial available, Available for purchase | SCR_015248 | Statgraphics Centurion XVII | 2026-02-15 09:21:22 | 7 | |||||||||
|
BLASTX Resource Report Resource Website 10000+ mentions |
BLASTX (RRID:SCR_001653) | BLASTX | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. | protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
PMID:28902395 PMID:8485583 |
Free, Freely Available | nlx_153933, OMICS_00992 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001653 | Translated BLAST, Translated BLAST: blastx | 2026-02-15 09:18:09 | 10091 | |||||
|
ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | database, service resource, storage service resource, data repository, data or information resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-02-15 09:18:11 | 53 | ||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | database, software resource, web service, data access protocol, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NIAID NO1-CO-56000; NCI |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-02-15 09:18:11 | 18488 | ||||
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GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | software application, software library, data processing software, software resource, software toolkit, data analysis software | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit https://bio.tools/gatk |
SCR_001876 | Genome Analysis ToolKit | 2026-02-15 09:18:11 | 16663 | |||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | software application, data processing software, data analysis software, software resource | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-02-15 09:18:10 | 9 | ||||
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FlowJo Resource Report Resource Website 10000+ mentions |
FlowJo (RRID:SCR_008520) | software application, data processing software, data analysis software, software resource | 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. | single-cell analysis, flow cytometry, flow cytometer, mass cytometer |
is listed by: SoftCite has plug in: SPADE has plug in: flowMeans has plug in: DownSample has plug in: FlowSOM |
nif-0000-30575 | SCR_008520 | FlowJo® | 2026-02-15 09:19:51 | 67274 | |||||||||
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EMBOSS Resource Report Resource Website 1000+ mentions |
EMBOSS (RRID:SCR_008493) | EMBOSS | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | 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. | FASEB list |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: BioExtract is related to: pepwheel |
DOI:10.1016/S0168-9525(00)02024-2 | Free, Freely available | OMICS_21165, nif-0000-30488 | https://sources.debian.org/src/emboss/ | http://www.emboss.org | SCR_008493 | The European Molecular Biology Open Software Suite, European Molecular Biology Open Software Suite | 2026-02-15 09:19:51 | 4543 | ||||
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Matplotlib Resource Report Resource Website 5000+ mentions |
Matplotlib (RRID:SCR_008624) | software library, software toolkit, software resource | Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots. | 2D plotting library, plot, histogram, power spectra, bar chart, error chart, scatter plot |
is used by: seaborn is listed by: SoftCite is related to: MNE software |
Free, Available for download, Freely available | nif-0000-31991 | http://matplotlib.sourceforge.net | SCR_008624 | MatPlotLib | 2026-02-15 09:19:33 | 8069 |
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