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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||
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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 | |||||
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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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FANTOM DB Resource Report Resource Website 10+ mentions |
FANTOM DB (RRID:SCR_002678) | FANTOM DB | biomaterial supply resource, material resource | The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN. | cdna clone, mouse, mouse cdna, human, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: CAGE has parent organization: RIKEN Omics Science Center |
PMID:20211142 | Free, Available for download, Freely available | nif-0000-02833, biotools:fantom | http://fantom3.gsc.riken.jp/, https://bio.tools/fantom | SCR_002678 | FANTOM: Functional Annotation of Mouse, FANTOM2, FANTOM1, Functional Annotation of the Mammalian Genome, FANTOM4, FANTOM3, FANTOM, Functional Annotation of Mouse | 2026-08-07 09:25:29 | 20 | |||||
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SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | commercial organization, software resource, software application | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-08-07 09:25:23 | 17 | |||||
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e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | standalone software, software resource, software application | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | 2026-08-07 09:25:29 | 5 | ||||||
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IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software resource, software application | 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 | 2026-08-07 09:25:32 | 625 | ||||||
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GoSurfer Resource Report Resource Website 1+ mentions |
GoSurfer (RRID:SCR_005789) | GoSurfer | software resource, software application | 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 | 2026-08-07 09:26:14 | 2 | |||||
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BOMP: beta-barrel Outer Membrane protein Predictor Resource Report Resource Website 1+ mentions |
BOMP: beta-barrel Outer Membrane protein Predictor (RRID:SCR_007268) | software resource, software application | 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 | 2026-08-07 09:26:31 | 5 | ||||||||
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VarScan Resource Report Resource Website 1000+ mentions |
VarScan (RRID:SCR_006849) | VarScan, VarScan 2 | software resource, software application | 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). | 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: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is organization facet of: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
Free, Available for download, Freely available | , 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, http://tvap.genome.wustl.edu/tools/varscan/ | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-08-07 09:26:25 | 1983 | ||||
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zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NIGMS GM63904; NIDA DA14546; NHGRI HG006431 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-08-07 09:26:25 | 4 | ||||
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LDSELECT Resource Report Resource Website 10+ mentions |
LDSELECT (RRID:SCR_007010) | LDSELECT | software resource, software application | 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 | 2026-08-07 09:26:29 | 15 | |||||||
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FASTSLINK Resource Report Resource Website 10+ mentions |
FASTSLINK (RRID:SCR_008664) | FASTSLINK | software resource, software application | Software application that is a faster version of SLINK (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: SLINK is related to: SUP |
nlx_154312, biotools:snpcaller | https://bio.tools/snpcaller | SCR_008664 | faster SLINK | 2026-08-07 09:26:47 | 12 | |||||||
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PEDPEEL Resource Report Resource Website |
PEDPEEL (RRID:SCR_008436) | PEDPEEL | software resource, software application | Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (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_154524, biotools:pedpeel | https://bio.tools/pedpeel | SCR_008436 | 2026-08-07 09:26:46 | 0 | ||||||||
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ADMIXMAP Resource Report Resource Website 10+ mentions |
ADMIXMAP (RRID:SCR_009035) | ADMIXMAP | software resource, software application | General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_153999, biotools:admixmap | https://bio.tools/admixmap | SCR_009035 | Admixture mapping | 2026-08-07 09:26:51 | 20 | |||||||
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PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software resource, software application | 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 | 2026-08-07 09:26:51 | 1 | ||||||||
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MOSCPHASER Resource Report Resource Website |
MOSCPHASER (RRID:SCR_009092) | MOSCPHASER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
PMID:18492685 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154109, biotools:mocsphaser | https://bio.tools/mocsphaser | http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip | SCR_009092 | Mixture Of Cnv-Snp PHASER | 2026-08-07 09:26:53 | 0 | ||||
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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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