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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-02-15 09:18:12 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo https://sources.debian.org/src/aragorn/ |
SCR_001936 | 2026-02-15 09:18:12 | 274 | ||||||
|
MRFSEQ Resource Report Resource Website |
MRFSEQ (RRID:SCR_002972) | algorithm resource, software resource | Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene. | markov, algorithm, gene expression, prediction algorithm, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
PMID:23793751 | Free, Available for download, Freely available | biotools:mrfseq, OMICS_01309 | https://bio.tools/mrfseq | SCR_002972 | 2026-02-15 09:18:25 | 0 | |||||||
|
IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast https://sources.debian.org/src/ncbi-igblast/ |
SCR_002873 | IgBLAST | 2026-02-15 09:18:24 | 609 | ||||||
|
GoSurfer Resource Report Resource Website 1+ mentions |
GoSurfer (RRID:SCR_005789) | GoSurfer | software application, software resource | GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible | gene, gene ontology, genome-wide, microarray, graph, data mining, statistical analysis, bioinformatics, genomics, gene cluster, multiple hypothesis testing, false discovery rate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA has parent organization: Harvard T.H. Chan School of Public Health |
PMID:15702958 | Free for academic use | biotools:gosurfer, nlx_149268 | http://www.gosurfer.org https://bio.tools/gosurfer |
http://bioinformatics.bioen.illinois.edu/gosurfer/index.htm | SCR_005789 | 2026-02-15 09:19:04 | 2 | |||||
|
BOMP: beta-barrel Outer Membrane protein Predictor Resource Report Resource Website 1+ mentions |
BOMP: beta-barrel Outer Membrane protein Predictor (RRID:SCR_007268) | software application, software resource | BOMP is a tool for prediction of beta-barrel integral outer membrane proteins. The user may submit a list of proteins, and receive a list of predicted BOMPs. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane -strands. To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially. Sponsors: This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU151899/ISO], and the Meltzer Foundation, University of Bergen. Keywords: Beta-barrel, Membrane, Protein, Program, Software, Beta strand, Bacteria, | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Bergen; Bergen; Norway |
biotools:bomp, nif-0000-30236 | https://bio.tools/bomp | SCR_007268 | BOMP Program | 2026-02-15 09:19:23 | 5 | ||||||||
|
VARSCAN Resource Report Resource Website 1000+ mentions |
VARSCAN (RRID:SCR_006849) | VarScan | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java, illumina, solid, life/pgm, roche/454, next-generation sequencing, variant, mutation caller, exome, whole-genome, snp, copy number alteration, somatic mutation, subclonal mutation, mutation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154687, biotools:varscan, OMICS_00094 | http://varscan.sourceforge.net/ http://dkoboldt.github.io/varscan/ https://bio.tools/varscan https://sources.debian.org/src/varscan/ |
http://genome.wustl.edu/software/varscan | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-02-15 09:19:20 | 1769 | ||||
|
LDSELECT Resource Report Resource Website 10+ mentions |
LDSELECT (RRID:SCR_007010) | LDSELECT | software application, software resource | Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ld_select, nlx_154426 | https://bio.tools/ld_select | SCR_007010 | 2026-02-15 09:19:21 | 15 | |||||||
|
Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software application, source code, software resource | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML https://sources.debian.org/src/examl/ |
SCR_016087 | Examl:Exascale Maximum Likelihood | 2026-02-15 09:21:46 | 60 | ||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-02-15 09:17:58 | 0 | ||||||
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VeryFastTree Resource Report Resource Website 1+ mentions |
VeryFastTree (RRID:SCR_023594) | software application, source code, software resource | Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies. | large alignments, phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: bio.tools is related to: FastTree |
MICINN ; Xunta de Galicia ; ERDF |
PMID:32573652 DOI:10.1093/bioinformatics/btaa582 |
Free, Available for download, Freely available | biotools:veryfasttree | https://bio.tools/veryfasttree | SCR_023594 | 2026-02-15 09:22:29 | 5 | ||||||
|
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 | |||||
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Telescope Resource Report Resource Website 1+ mentions |
Telescope (RRID:SCR_017626) | web application, software resource | Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted. | Track, progress, remote, server, scheduling, system, on demand, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Los Angeles; California; USA |
Free, Freely available | biotools:telescope | https://bio.tools/Telescope | SCR_017626 | 2026-02-15 09:22:10 | 2 | ||||||||
|
Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | data or information resource, database, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package https://sources.debian.org/src/vienna-rna/ |
SCR_008550 | Vienna RNA | 2026-02-15 09:19:51 | 404 | |||||||
|
BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-02-15 09:19:57 | 39 | ||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-02-15 09:19:00 | 37 | ||||||
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Database of Secondary Structure Assignments Resource Report Resource Website 50+ mentions |
Database of Secondary Structure Assignments (RRID:SCR_002725) | DSSP | data or information resource, database, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command. | amino acid sequence, hydrogen bonding, protein conformation, proteins, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:6667333 PMID:21071423 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23901, biotools:dssp, OMICS_06247 | http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+DSSP https://bio.tools/dssp https://sources.debian.org/src/dssp/ |
http://www.sander.ebi.ac.uk/dssp/ | SCR_002725 | 2026-02-15 09:18:23 | 59 | |||||
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Segway - a way to segment the genome Resource Report Resource Website 1+ mentions |
Segway - a way to segment the genome (RRID:SCR_004206) | source code, software resource | The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind. | genome annotation, source code, bayesian network model, bayesian, chip seq, dbn, bio.tools |
is used by: ENCODE is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA has parent organization: University of Toronto; Ontario; Canada |
PMID:22426492 | Free | nlx_22911, biotools:segway | https://www.pmgenomics.ca/hoffmanlab/proj/segway/ https://bitbucket.org/hoffmanlab/segway/ https://bio.tools/segway |
http://noble.gs.washington.edu/proj/segway/ | SCR_004206 | Segway | 2026-02-15 09:18:39 | 8 | |||||
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CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | source code, software resource | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-02-15 09:19:58 | 5 | |||||
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PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software application, software resource | Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-02-15 09:20:02 | 1 |
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