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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data management software, data or information resource, database, software application, software resource | Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data. | connectome file format, clinical neuroinformatics, computational neuroscience, computed tomography, imaging genomics, interfile, javascript, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:25888923 | Free, Available for download, Freely available | nlx_155882 | http://www.nitrc.org/projects/nidb | http://nidb.sourceforge.net/ | SCR_002488 | Neuroinformatics Database | 2026-08-29 11:21:06 | 2 | ||||
|
SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-08-29 11:21:16 | 17 | ||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | data analysis software, data processing software, software application, software resource, software toolkit | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-08-29 11:21:14 | 26 | ||||||
|
GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | 2026-08-29 11:21:19 | 1 | ||||||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-08-29 11:21:11 | 41 | ||||||
|
rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | 2026-08-29 11:21:20 | 122 | ||||||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-08-29 11:21:41 | 0 | ||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-08-29 11:20:33 | 3 | |||||
|
detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | detecttd - Tool to detect tandem duplications in NGS reads | 2026-08-29 11:20:29 | 0 | |||||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-08-29 11:20:34 | 4 | ||||||||
|
TriageTools Resource Report Resource Website |
TriageTools (RRID:SCR_000675) | TriageTools | software resource | A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. | matlab, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23408855 | Free, Available for download, Freely available | biotools:triagetools, nlx_156740 | https://bio.tools/triagetools | SCR_000675 | 2026-08-29 11:20:45 | 0 | ||||||
|
NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-08-29 11:20:44 | 3 | |||||||
|
Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | OPERA-LG, Optimal Paired-End Read Assembler | 2026-08-29 11:20:29 | 3 | ||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-08-29 11:20:42 | 0 | |||||||
|
PHACCS Resource Report Resource Website 1+ mentions |
PHACCS (RRID:SCR_001232) | software resource | Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15743531 | Free, Available for download, Freely available | OMICS_03529 | SCR_001232 | 2026-08-29 11:20:47 | 1 | ||||||||
|
QUAST Resource Report Resource Website 1000+ mentions |
QUAST (RRID:SCR_001228) | QUAST | software resource | Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots. | genome assembly, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia has parent organization: SourceForge |
PMID:23422339 | biotools:quast, OMICS_02115 | https://bio.tools/quast, https://sources.debian.org/src/quast/ | SCR_001228 | QUAST: Quality Assessment Tool for Genome Assemblies | 2026-08-29 11:21:00 | 3293 | ||||||
|
Mutascope Resource Report Resource Website 1+ mentions |
Mutascope (RRID:SCR_001265) | Mutascope | data analysis software, data processing software, software application, software resource | Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. | high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variant |
is listed by: OMICtools has parent organization: SourceForge |
Tumor, Normal | PMID:23712659 | Free, Public | OMICS_02074 | SCR_001265 | Mutascope - Analysis software designed for PCR-amplicon sequencing data | 2026-08-29 11:20:48 | 4 | |||||
|
KAnalyze Resource Report Resource Website 1+ mentions |
KAnalyze (RRID:SCR_001323) | software resource | A Java toolkit designed to convert DNA and RNA sequences into k-mers. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24642064 | Free, Available for download, Freely available | biotools:kanalyze, OMICS_03565 | https://bio.tools/kanalyze | SCR_001323 | 2026-08-29 11:20:41 | 2 | |||||||
|
Mugsy Resource Report Resource Website 50+ mentions |
Mugsy (RRID:SCR_001414) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. | software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:21148543 DOI:10.1093/bioinformatics/btq665 |
Free, Available for download, Freely available | OMICS_03606 | https://sources.debian.org/src/mugsy/ | SCR_001414 | 2026-08-29 11:20:53 | 75 | |||||||
|
Drosophila anatomy and development ontologies Resource Report Resource Website |
Drosophila anatomy and development ontologies (RRID:SCR_001607) | FBbt | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems. | anatomy, development, developmental stage, gene expression, phenotype, owl |
is related to: OBO is related to: Flannotator is related to: REDfly Regulatory Element Database for Drosophilia is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: FlyBase has parent organization: SourceForge |
NHGRI P41 HG000739 | Free, Freely available | nlx_153871 | SCR_001607 | Drosophila anatomy & dev ontologies | 2026-08-29 11:20:46 | 0 |
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