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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | 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) | 2026-09-12 12:58:20 | 139 | |||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data analysis software, data management software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:18 | 19827 | |||||||
|
Brain Extraction Tool Resource Report Resource Website 10+ mentions |
Brain Extraction Tool (RRID:SCR_014586) | BET2, BET | data processing software, image processing software, software application, 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) | 2026-09-12 12:58:18 | 17 | |||||||
|
NVivo Resource Report Resource Website 10000+ mentions |
NVivo (RRID:SCR_014802) | data analysis software, data processing software, software application, 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 | 2026-09-12 12:58:22 | 13145 | |||||||||||
|
Simulink Resource Report Resource Website 100+ mentions |
Simulink (RRID:SCR_014744) | simulation software, software application, software resource, software toolkit | 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 | 2026-09-12 12:58:21 | 396 | ||||||||||
|
MOE Resource Report Resource Website 10+ mentions |
MOE (RRID:SCR_014882) | software resource | Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis. | drug discovery, software package, structure based design, fragment based design, pharmacophore, medicinal chemistry, protein modeling, antibody modeling, molecular modeling, molecular simulations | is listed by: SoftCite | SCR_014882 | 2026-09-12 12:58:22 | 27 | |||||||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | 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 | 2026-09-12 12:58:20 | 1993 | |||||
|
WinWCP Resource Report Resource Website 100+ mentions |
WinWCP (RRID:SCR_014713) | data acquisition software, data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:58:21 | 435 | |||||||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-09-12 12:57:40 | 24687 | |||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-09-12 12:57:39 | 310 | |||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-09-12 12:57:40 | 772 | |||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-09-12 12:57:56 | 38 | ||||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-09-12 12:58:01 | 1418 | ||||
|
BioMoby Resource Report Resource Website 1+ mentions |
BioMoby (RRID:SCR_013386) | controlled vocabulary, data or information resource, ontology | The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics, |
is listed by: SoftCite is related to: BioExtract has parent organization: Pompeu Fabra University; Barcelona; Spain |
nif-0000-30186 | SCR_013386 | BioMoby | 2026-09-12 12:58:02 | 8 | ||||||||||
|
TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Howard Hughes Medical Institute ; NIGMS GM067031; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-09-12 12:57:24 | 11785 | |||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | 2026-09-12 12:57:26 | 397 | |||||||||
|
NIA Array Analysis Resource Report Resource Website 50+ mentions |
NIA Array Analysis (RRID:SCR_010948) | NIA Array Analysis | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource, software resource | Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available. | gene expression, microarray, principal component analysis, significance analysis, gene annotation, anova, hierarchical clustering, pattern matching |
is listed by: OMICtools is listed by: SoftCite has parent organization: National Institute on Aging |
PMID:15734774 | OMICS_00774 | SCR_010948 | 2026-09-12 12:57:26 | 50 | ||||||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | analysis service resource, data analysis service, production service resource, service resource, software resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-09-12 12:57:42 | 687 | |||||
|
AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-09-12 12:57:43 | 2447 | ||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-12 12:57:44 | 10714 |
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