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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SNAVI Resource Report Resource Website |
SNAVI (RRID:SCR_000091) | software resource | Desktop application for analysis and visualization of large-scale cell signaling networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:19154595 | Free, Available for download, Freely available | biotools:snavi, OMICS_04122 | https://bio.tools/snavi | SCR_000091 | Signaling Networks Analysis and Visualization | 2026-08-01 12:01:08 | 0 | ||||||
|
Megraft Resource Report Resource Website |
Megraft (RRID:SCR_000240) | Megraft | software resource | A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. | windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22824070 | Free, Available for download, Freely available | biotools:megraft, OMICS_02161 | https://bio.tools/megraft | SCR_000240 | 2026-08-01 12:01:14 | 0 | ||||||
|
VARiD Resource Report Resource Website |
VARiD (RRID:SCR_000241) | VARiD | software resource | Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads. | c, single nucleotide polymorphism, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20529926 | Free, Available for download, Freely available | OMICS_02163, biotools:varid | https://bio.tools/varid | SCR_000241 | 2026-08-01 12:01:12 | 0 | ||||||
|
TAPIR: target prediction for plant microRNAs Resource Report Resource Website 10+ mentions |
TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) | TAPIR | Web server designed for prediction of plant microRNA targets. | prediction of plant microRNA targets, microrna, target, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:20430753 | biotools:tapir, OMICS_04004 | https://bio.tools/tapir | SCR_000237 | 2026-08-01 12:01:10 | 10 | ||||||||
|
SODOCK Resource Report Resource Website 1+ mentions |
SODOCK (RRID:SCR_000193) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. | particle swarm optimization, protein, ligand, docking, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:17186483 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:sodock, OMICS_01606 | https://bio.tools/sodock | SCR_000193 | 2026-08-01 12:01:12 | 1 | |||||||
|
Quant Resource Report Resource Website |
Quant (RRID:SCR_000267) | software resource | A software tool for the proteomics community that may help improving analysis of proteomic experimental data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17584939 | Free, Available for download, Freely available | OMICS_02504, biotools:quant | https://bio.tools/quant | SCR_000267 | 2026-08-01 12:01:10 | 0 | |||||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | 2026-08-01 12:01:10 | 4 | |||||||
|
GraphProt Resource Report Resource Website 10+ mentions |
GraphProt (RRID:SCR_005842) | GraphProt | software resource | Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. | sequence-binding preference, structure-binding preference, rna-binding protein, high-throughput sequencing, clip-seq, rnacompete, rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:24451197 | Free, Public | OMICS_02252, biotools:graphprot | https://bio.tools/graphprot | SCR_005842 | 2026-08-01 12:03:02 | 36 | ||||||
|
Cascade Resource Report Resource Website 50+ mentions |
Cascade (RRID:SCR_005861) | Cascade | software resource | R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, windows, gene expression, perturbation, network, diffusion, signal, temporal gene network, gene regulatory network, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:24307703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02249, biotools:cascade | http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4, https://bio.tools/cascade | SCR_005861 | 2026-08-01 12:03:00 | 92 | ||||||
|
BiNGO: A Biological Networks Gene Ontology tool Resource Report Resource Website 500+ mentions |
BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) | BiNGO | software resource | The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, ontology, statistical analysis, term enrichment, biological network, plugin, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:15972284 | Open unspecified license - Free for academic use | nlx_149196, biotools:bingo | https://bio.tools/bingo | SCR_005736 | Biological Networks Gene Ontology | 2026-08-01 12:02:58 | 790 | |||||
|
h5vc Resource Report Resource Website 1+ mentions |
h5vc (RRID:SCR_006039) | h5vc | software resource | Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:24451629 | GNU General Public License, v3 or newer | biotools:h5vc, OMICS_02243 | http://www.ebi.ac.uk/~pyl/h5vc/, https://bio.tools/h5vc | SCR_006039 | h5vc - Scalable nucleotide tallies with HDF5, h5vc - Managing alignment tallies using a hdf5 backend | 2026-08-01 12:03:03 | 2 | |||||
|
IRanges Resource Report Resource Website 50+ mentions |
IRanges (RRID:SCR_006420) | IRanges | software resource | Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible. | Annotating genomic ranges, computing genomic ranges, genomic ranges, storing ranges of integers, bio.tools |
is used by: riboWaltz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23950696 | Free, Available for download, Freely available | OMICS_01163, biotools:iranges | https://bio.tools/iranges | SCR_006420 | Infrastructure for manipulating intervals on sequences | 2026-08-01 12:03:09 | 77 | |||||
|
VICUNA Resource Report Resource Website 10+ mentions |
VICUNA (RRID:SCR_006302) | VICUNA | software resource | A de novo assembly program targeting populations with high mutation rates. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:22974120 | biotools:vicuna, OMICS_02162 | https://bio.tools/vicuna | SCR_006302 | 2026-08-01 12:03:08 | 26 | |||||||
|
MSIsensor Resource Report Resource Website 100+ mentions |
MSIsensor (RRID:SCR_006418) | MSIsensor | software resource | A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. | c++, somatic variant, germline variant, microsatellite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Tumor, Normal | PMID:24371154 | Copyrighted, See LICENSE | biotools:msisensor, OMICS_02192 | https://bio.tools/msisensor | SCR_006418 | 2026-08-01 12:03:08 | 156 | |||||
|
TSSer Resource Report Resource Website |
TSSer (RRID:SCR_006419) | TSSer | software resource | A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide. | differential rna sequencing, transcription start site, rna-seq, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Basel; Basel; Switzerland |
PMID:24371151 | GNU General Public License | biotools:tsser, OMICS_02191 | https://bio.tools/tsser | SCR_006419 | TSSer: a computational pipeline to identify transcription start sites in bacterial genomes | 2026-08-01 12:03:11 | 0 | |||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-08-01 12:03:09 | 18 | |||||
|
FLUX CAPACITOR Resource Report Resource Website 1+ mentions |
FLUX CAPACITOR (RRID:SCR_006651) | FLUX CAPACITOR | software resource | Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20220756 | biotools:the_flux_capacitor, OMICS_01293 | https://bio.tools/the_flux_capacitor | SCR_006651 | The FLUX CAPACITOR, FluxCapacitor | 2026-08-01 12:03:14 | 2 | ||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-08-01 12:08:11 | 0 | ||||||
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software toolkit, software resource | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-08-02 09:02:53 | 5 | |||||||
|
Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software toolkit, software resource | A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated. | bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1038/NMETH.1818 | nlx_156936, OMICS_28407, biotools:bioinformatics_toolkit | https://bio.tools/bioinformatics_toolkit, https://sources.debian.org/src/hhsuite/ | SCR_010277 | 2026-08-02 09:05:41 | 235 |
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