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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NCBI Structure: Cn3D Resource Report Resource Website 100+ mentions |
NCBI Structure: Cn3D (RRID:SCR_004861) | d visualization software | Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains. | gold standard, bio.tools |
is listed by: bio.tools is related to: NCBI Structure has parent organization: NCBI |
PMID:10838572 | biotools:cn3d, nlx_84208 | https://bio.tools/cn3d | SCR_004861 | Cn3D | 2026-02-14 02:00:45 | 130 | |||||||
|
MetaPhyler Resource Report Resource Website 10+ mentions |
MetaPhyler (RRID:SCR_004848) | software resource | A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. | metagenome, classification, sequence, taxonomy, genome, microbiome, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21989143 | Acknowledgement requested, Available for download | OMICS_01455, biotools:metaphyler | https://bio.tools/metaphyler | SCR_004848 | MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences | 2026-02-14 02:00:48 | 11 | ||||||
|
hyfi: software suite for binding site search Resource Report Resource Website |
hyfi: software suite for binding site search (RRID:SCR_004884) | software resource | This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:16873493 | nlx_85657, biotools:hyfi | https://bio.tools/hyfi | SCR_004884 | Hyfi | 2026-02-14 02:01:02 | 0 | |||||||
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-02-14 02:00:59 | 124 | ||||||||
|
miRNAKey Resource Report Resource Website 1+ mentions |
miRNAKey (RRID:SCR_004813) | miRNAKey | software resource | A software pipeline for the analysis of microRNA Deep Sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20801911 | OMICS_00364, biotools:mirnakey | https://bio.tools/mirnakey | SCR_004813 | 2026-02-14 02:00:45 | 6 | |||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-02-14 02:00:47 | 19 | ||||||
|
SVseq Resource Report Resource Website 1+ mentions |
SVseq (RRID:SCR_004804) | SVseq | software resource | Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions. | structural variant, deletion, insertion, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Connecticut; Connecticut; USA |
PMID:22537045 | OMICS_00327, biotools:svseq | https://bio.tools/svseq | SCR_004804 | SVseq2, SVseq1 | 2026-02-14 02:00:45 | 3 | ||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia https://sources.debian.org/src/minia/ |
SCR_004986 | 2026-02-14 02:00:47 | 62 | |||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-02-14 02:01:02 | 1 | ||||||||
|
OLego Resource Report Resource Website 10+ mentions |
OLego (RRID:SCR_005811) | OLego | software resource | A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
biotools:olego, OMICS_01244 | https://bio.tools/olego | SCR_005811 | 2026-02-14 02:01:11 | 15 | ||||||||
|
PePr Resource Report Resource Website 50+ mentions |
PePr (RRID:SCR_005759) | PePr | software resource | A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24894502 | GNU General Public License, v3 | OMICS_04058, biotools:pepr | https://bio.tools/pepr | SCR_005759 | pepr-chip-seq, Peak Prioritization Pipeline, pepr-chip-seq: A ChIP-Seq analyzing program for biological replicates | 2026-02-14 02:00:58 | 53 | |||||
|
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 | 2026-02-14 02:00:59 | 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 | 2026-02-14 02:01:12 | 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 | 2026-02-14 02:01:00 | 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 | 2026-02-14 02:01:01 | 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 | 2026-02-14 02:01:18 | 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 | 2026-02-14 02:01:15 | 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 | 2026-02-14 02:01:17 | 156 | |||||
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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 | 2026-02-14 02:01:09 | 0 | |||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-02-14 02:00:52 | 2 |
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