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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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qcat Resource Report Resource Website 10+ mentions |
qcat (RRID:SCR_024195) | software resource, software application | Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. | command-line tool, demultiplexing Oxford Nanopore reads, reads from FASTQ files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qcat/ | SCR_024195 | 2026-08-07 09:30:11 | 22 | |||||||||
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MacSyFinder Resource Report Resource Website 10+ mentions |
MacSyFinder (RRID:SCR_024106) | software resource, software application | Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search. | Detection of macromolecular system, protein datasets, mine genomes, molecular systems, | is listed by: Debian | PMID:25330359 | Free, Available for download, Freely available, | OMICS_20116 | https://sources.debian.org/src/macsyfinder/ | SCR_024106 | macsyfinder | 2026-08-07 09:30:10 | 28 | ||||||
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tiddit Resource Report Resource Website 1+ mentions |
tiddit (RRID:SCR_024361) | software resource, software application | Software tool as structural variant calling. | structural variant calling, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tiddit/ | SCR_024361 | TIDDIT | 2026-08-07 09:30:15 | 3 | ||||||||
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Yanagiba Resource Report Resource Website |
Yanagiba (RRID:SCR_024362) | software resource, software application | Software tool to filter and slice Nanopore reads which have been basecalled with Albacore. | filter and slice Nanopore reads, basecalled with Albacore, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanagiba/ | SCR_024362 | yanagiba | 2026-08-07 09:30:13 | 0 | ||||||||
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Nanocall Resource Report Resource Website |
Nanocall (RRID:SCR_024124) | software resource, software application | Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller. | basecaller, Oxford Nanopore Technologies, sequencing data, | is listed by: Debian | PMID:27614348 | Free, Available for download, Freely available, | OMICS_11495 | https://sources.debian.org/src/nanocall/ | SCR_024124 | Nanocall, nanocall | 2026-08-07 09:30:10 | 0 | ||||||
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swarm Resource Report Resource Website 1+ mentions |
swarm (RRID:SCR_024358) | software resource, software application | Software tool as clustering method for amplicon-based studies. | clustering method, amplicon based studies, | is listed by: Debian | PMID:26713226 | Free, Available for download, Freely available, | OMICS_14578 | https://sources.debian.org/src/swarm/ | SCR_024358 | 2026-08-07 09:30:13 | 5 | |||||||
|
Segway - a way to segment the genome Resource Report Resource Website 10+ mentions |
Segway - a way to segment the genome (RRID:SCR_004206) | software resource, source code | 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 | 2026-08-07 09:25:50 | 10 | |||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-08-07 09:26:22 | 15653 | ||||||||
|
Biopieces Resource Report Resource Website 10+ mentions |
Biopieces (RRID:SCR_005783) | Biopieces | software resource, software toolkit, source code | A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014). | bioinformatics, tool, framework, biopieces, language independent, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Project Hosting |
Danish Agency for Science Technology and Innovation 272-06-0325 | GNU General Public License, v2 | nlx_149253, biotools:biopieces, OMICS_01036 | http://code.google.com/p/biopieces/, https://bio.tools/biopieces | SCR_005783 | www.biopieces.org, biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created | 2026-08-07 09:26:10 | 40 | |||||
|
VIDA Resource Report Resource Website 100+ mentions |
VIDA (RRID:SCR_007111) | VIDA | data or information resource, data set | VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, users can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. * Search homologous protein families from particular virus families * Links to complete genome sequence: Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomics, non-vertebrate, viral genome, homologous protein, hpf, viral genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
BBSRC ; MRC |
PMID:11125070 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03628, biotools:vida | https://bio.tools/vida | http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html | SCR_007111 | Virus Database at University College London, Virus Database, VIDA Virus Database | 2026-08-07 09:26:29 | 193 | |||
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CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | 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) | 2026-08-07 09:26:50 | 5 | |||||
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FusionHunter Resource Report Resource Website 1+ mentions |
FusionHunter (RRID:SCR_011895) | FusionHunter | software resource, source code | Software for identifying fusion transcripts using paired-end RNA-seq. | perl, annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01350, biotools:fusionhunter | https://bio.tools/fusionhunter | SCR_011895 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-08-07 09:27:31 | 8 | |||||||
|
SAM Resource Report Resource Website 100+ mentions |
SAM (RRID:SCR_010951) | software resource | Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments. | genomic expression, data mining, finding significant genes, microarray experiments, |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: pysam has parent organization: Stanford University; Stanford; California |
Commercial use requires license, Registration required | OMICS_01314, OMICS_00779, SCR_011888 | https://sources.debian.org/src/r-cran-samr/ | SCR_010951 | SAM: Significance Analysis of Microarrays, Significance Analysis of Microarrays | 2026-08-07 09:27:22 | 235 | |||||||
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GLUE Resource Report Resource Website 10+ mentions |
GLUE (RRID:SCR_009211) | GLUE | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, perl, any web browser, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154360, biotools:GLUE | https://bio.tools/GLUE | http://portal.litbio.org/Registered/Webapp/glue/ | SCR_009211 | Genetic Linkage User Environment | 2026-08-07 09:26:54 | 46 | |||||
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TWOLOC Resource Report Resource Website |
TWOLOC (RRID:SCR_009230) | TWOLOC | software resource, software application | Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77, pascal, awk, unix, (saloris/dec unix/irix/..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154387, biotools:twoloc | https://bio.tools/twoloc | SCR_009230 | 2026-08-07 09:26:55 | 0 | ||||||||
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GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software resource, software application | Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-08-07 09:26:59 | 1 | ||||||||
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HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software resource, software application | Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-08-07 09:27:00 | 1 | |||||||
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MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software resource, software application | A multipoint linkage analysis software which allows Marker-Marker LD (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_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-08-07 09:27:02 | 0 | ||||||||
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MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software resource, software application | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-08-07 09:26:59 | 12 | |||||||
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Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software resource, software toolkit | 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 | 2026-08-07 09:27:16 | 261 |
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