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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AfterQC Resource Report Resource Website 10+ mentions |
AfterQC (RRID:SCR_016390) | software resource, data processing software, software application | Software that performs automatic filtering, trimming, error removing, and quality control for fastq data. | fastq, qc, editing, filtering, trimming, dna, rna, seq, sequence, sequencing, poly, pair-end, python | PMID:28361673 | Free, Available for download | SCR_016390 | After QC | 2026-08-02 09:07:19 | 14 | |||||||||
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Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | software toolkit, software resource, data processing software, alignment software, software application, image analysis software | Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads. | Overlapping, patching, correction, assembly, noisy, long, read, sequence, align | Free, Available for download, Freely available | SCR_017621 | 2026-08-02 09:07:43 | 2 | |||||||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, software resource, data processing software, software application | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-02 09:07:35 | 2899 | |||||
|
PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | web service, software resource, production service resource, data access protocol, data or information resource, database, service resource, analysis service resource | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-08-02 09:07:27 | 4 | ||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | software resource, production service resource, data or information resource, data processing software, alignment software, service resource, portal, software application, image analysis software, analysis service resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHMRC ; MESR ; CNRS ; Université Montpellier 2 ; France ; GENCI |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-08-02 09:07:41 | 11 | |||||
|
SignalP Resource Report Resource Website 5000+ mentions |
SignalP (RRID:SCR_015644) | web application, software resource | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-02 09:07:12 | 9406 | |||||||||
|
DynaMine Resource Report Resource Website 10+ mentions |
DynaMine (RRID:SCR_014559) | web application, software resource | An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nmr, protein folding, prediction, fasta, sequence, dynamics | PMID:24225580 | THIS RESOURCE IS NO LONGER IN SERVICE | http://dynamine.ibsquare.be | SCR_014559 | 2026-08-02 09:06:38 | 39 | |||||||||
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LINUCS Resource Report Resource Website |
LINUCS (RRID:SCR_001571) | LINUCS | software resource, production service resource, service resource, source code, data analysis service, analysis service resource | Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated | carbohydrate, notation, structure, carbohydrate sequence, canonical description, glycodatabase, glycobioinformatics, algorithm, molecule, sequence |
is related to: sumo is related to: pdb2linucs has parent organization: glycosciences.de |
PMID:11675023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152883 | SCR_001571 | LINUCS: LInear Notation for Unique description of Carbohydrate Sequences, LInear Notation for Unique description of Carbohydrate Sequences | 2026-08-02 09:03:16 | 0 | ||||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | production service resource, data or information resource, database, service resource, data analysis service, analysis service resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-08-02 09:03:17 | 3 | ||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | software resource, data or information resource, data visualization software, data processing software, database, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-08-02 09:03:26 | 0 | ||||||||
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HCV Databases Resource Report Resource Website 50+ mentions |
HCV Databases (RRID:SCR_002863) | HCV Databases | disease-related portal, data or information resource, topical portal, portal | The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. | hcv, hepatitis c virus, hepatitis c, database, data analysis service, sequence, immunology, annotation, FASEB list |
has parent organization: HIV Databases is parent organization of: HCV Sequence Database is parent organization of: HCV Immunology Database |
Hepatitis C | NIAID | Free, Freely available | nif-0000-02944 | SCR_002863 | Hepatitis C Virus Database, Hepatitis C Virus Database Project, HCV Database, Hepatitis C Virus Databases, Hepatitis C Virus (HCV) Database Project | 2026-08-02 09:03:46 | 66 | |||||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | production service resource, data or information resource, ontology, controlled vocabulary, database, data repository, service resource, storage service resource, data analysis service, analysis service resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-08-02 09:04:14 | 646 | ||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | software resource, data processing software, software application, data analysis software, image analysis software | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-08-02 09:05:00 | 8694 | |||||
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Albacore Resource Report Resource Website 100+ mentions |
Albacore (RRID:SCR_015897) | software resource, data processing software, software application | Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. | sequence, dna, raw data, event detection, single-read, nanopore, basecaller, basecaller software, dockerfile | Free, Available for download | SCR_015897 | 2026-08-02 09:07:13 | 427 | |||||||||||
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Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software resource, data processing software, software application | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-08-02 09:07:51 | 149 | ||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | standalone software, software resource, data processing software, software application | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-02 09:07:36 | 1309 | |||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software resource, data processing software, software application | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-08-02 09:07:36 | 2 | |||||
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ExonerateTransferAnnotation Resource Report Resource Website |
ExonerateTransferAnnotation (RRID:SCR_017557) | software resource, data processing software, software application | Software tool as pipeline to make anntotations using cDNA and CDS sequences. | Exonerate, transfer, annotation, cDNA, CDS, sequence, pipeline, gene | uses: Exonerate | Free, Available for download, Freely available | SCR_017557 | Resource | 2026-08-02 09:07:50 | 0 | |||||||||
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Augur Resource Report Resource Website 50+ mentions |
Augur (RRID:SCR_023964) | software toolkit, software resource | Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines. | track evolution, sequence, serological data. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/augur/, https://docs.nextstrain.org/projects/augur/en/stable/ | SCR_023964 | augur | 2026-08-02 09:09:08 | 67 | ||||||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | database, data or information resource | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-08-02 09:03:01 | 2 |
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