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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GASSST Resource Report Resource Website 1+ mentions |
GASSST (RRID:SCR_004413) | GASSST | software resource | Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Rennes 1; Rennes; France |
PMID:20739310 | CeCILL license, v2 | biotools:gassst, OMICS_00663 | https://bio.tools/gassst | SCR_004413 | SciCrunch Registry | GASSST : Global Alignment Short Sequence Search Tool, Global Alignment Short Sequence Search Tool | 2026-10-10 12:36:54 | 7 | |||||
|
Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | analysis service resource, data analysis service, production service resource, service resource, software resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | SciCrunch Registry | Trex-online | 2026-10-10 12:37:14 | 33 | ||||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NCRR P41 RR024851; NHGRI R01 HG003647; Sloan Foundation |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | SciCrunch Registry | Velvet Single Cell | 2026-10-10 12:37:10 | 5 | |||||
|
RAIphy Resource Report Resource Website 1+ mentions |
RAIphy (RRID:SCR_004720) | RAIphy | software resource | A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units. | classification, metagenome, phylogenetic profile, genome, taxonomic classification, dna sequence, relative abundance index |
is listed by: OMICtools has parent organization: University of Nebraska; Nebraska; USA |
PMID:21281493 | OMICS_01464 | SCR_004720 | SciCrunch Registry | 2026-10-10 12:36:52 | 3 | ||||||||
|
BioDiscovery Nexus Copy Number Resource Report Resource Website 100+ mentions |
BioDiscovery Nexus Copy Number (RRID:SCR_004557) | BioDiscovery | data analysis software, data analytics software, data processing software, software application, software resource | Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON. | Derives copy number, BAF, NGS data, WES, WGS, targeted panel, shallow sequencing, microarray data | is listed by: OMICtools | Commercially available | OMICS_01122 | http://www.biodiscovery.com/software/nexus-expression/ | SCR_004557 | SciCrunch Registry | Nexus Copy Number | 2026-10-10 12:36:57 | 168 | ||||||
|
ProViDE Resource Report Resource Website 100+ mentions |
ProViDE (RRID:SCR_004709) | ProViDE | software resource | A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, virus | is listed by: OMICtools | PMID:21544173 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01463 | SCR_004709 | SciCrunch Registry | ProViDE: Program for Viral Diversity Estimation, Program for Viral Diversity Estimation | 2026-10-10 12:37:00 | 279 | ||||||
|
TAIR Resource Report Resource Website 5000+ mentions |
TAIR (RRID:SCR_004618) | TAIR, AGI LocusCode | data or information resource, database | Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided. | genetic, molecular biology, gene, genome, structure, product, metabolism, gene expression, dna, seed stock, genome map, genetic marker, physical marker, genome sequence, gene product, blast, experimental protocol, gold standard |
is used by: NIF Data Federation is listed by: OMICtools is listed by: re3data.org is listed by: DataCite is related to: AmiGO is related to: Saskatoon Arabidopsis T-DNA mutant population SK Collection is related to: CLENCH has parent organization: Carnegie Institution for Science is parent organization of: TAIR Keyword Browser is parent organization of: PubSearch |
NSF DBI-0850219; corporate and nonprofit organizations |
PMID:22140109 PMID:17986450 PMID:12444417 PMID:12519987 PMID:18287693 |
r3d100010185, nlx_61477, OMICS_01662 | https://doi.org/10.17616/R3QW21 | SCR_004618 | SciCrunch Registry | AGI LocusCode, The Arabidopsis Information Resource | 2026-10-10 12:36:51 | 9170 | |||||
|
CompostBin Resource Report Resource Website 1+ mentions |
CompostBin (RRID:SCR_004619) | CompostBin | software resource | A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins. | metagenome, classification, read |
is listed by: OMICtools has parent organization: University of California at Davis; California; USA |
OMICS_01472 | SCR_004619 | SciCrunch Registry | 2026-10-10 12:36:58 | 3 | |||||||||
|
Distributed String Mining Framework Resource Report Resource Website 1+ mentions |
Distributed String Mining Framework (RRID:SCR_004736) | dsm-framework | software resource | Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24845653 | GNU General Public License, v2 or greater | biotools:dsm, OMICS_04171 | https://bio.tools/dsm | SCR_004736 | SciCrunch Registry | 2026-10-10 12:36:52 | 1 | ||||||
|
DELLY Resource Report Resource Website 500+ mentions |
DELLY (RRID:SCR_004603) | DELLY | software resource | Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome. | structural variant, genomic rearrangement, deletion, tandem duplication, inversion, translocation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
PMID:22962449 DOI:10.1093/bioinformatics/bts378 |
OMICS_00313, biotools:delly2 | https://bio.tools/delly2, https://github.com/dellytools/delly/, https://sources.debian.org/src/delly/ | SCR_004603 | SciCrunch Registry | DELLY, Structural variant discovery by integrated paired-end and split-read analysis | 2026-10-10 12:36:51 | 639 | ||||||
|
MetaCluster-TA Resource Report Resource Website 1+ mentions |
MetaCluster-TA (RRID:SCR_004599) | MetaCluster-TA | software resource | A software for binning and annotating short paired-end reads. | binning, annotation, metagenomics | is listed by: OMICtools | PMID:24564377 | OMICS_01473 | SCR_004599 | SciCrunch Registry | 2026-10-10 12:36:58 | 4 | ||||||||
|
tree editor Resource Report Resource Website |
tree editor (RRID:SCR_004533) | tred | software resource | Software tool to visualize and edit phylogenetic trees. It combines a browser-based Javascript client with a Python (web2py) server. Trees are rendered in SVG using Raphael. | phylogenetics, python, javascript, web2py, svg |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v3 | OMICS_04262 | SCR_004533 | SciCrunch Registry | tred: web-based visualization and editing of phylogenetic trees | 2026-10-10 12:37:15 | 0 | |||||||
|
LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | SciCrunch Registry | Livermore Metagenomics Analysis Toolkit | 2026-10-10 12:37:17 | 15 | ||||||
|
DiScRIBinATE Resource Report Resource Website 1+ mentions |
DiScRIBinATE (RRID:SCR_004862) | DiScRIBinATE | software resource | Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program. | metagenome, classification, sequence | is listed by: OMICtools | PMID:21106121 | Free for academic use, Non-commercial, Commercial use with permission, Acknowledgement requested, Copyright - Tata Consultancy Services | OMICS_01453 | SCR_004862 | SciCrunch Registry | DiScRIBinATE: Distance Score Ratio for Improved Binning and Taxonomic Estimation, Distance Score Ratio for Improved Binning and Taxonomic Estimation | 2026-10-10 12:37:23 | 4 | ||||||
|
MARTA Resource Report Resource Website 10+ mentions |
MARTA (RRID:SCR_004850) | MARTA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Java-based software that blasts each sequence that you provide it, and then looks for a consensus taxon among the top-hits returned from blast. MARTA uses NCBI''s megablast program to align your sequence(s) against a local installation of blast. Then MARTA uses GenInfo Identifiers from the top-hits to retrieve taxonomic information from NCBI''s taxonomy database. Using your thresholds/cutoffs, MARTA ''votes'' to find a taxonomic assignment by consensus; MARTA might resolve some sequences to species level, and others to kingdom or to no level, depending on the taxonomic information held within your tag or sequence. | taxonomy, java, metagenome, rdna, taxonomic assignment |
is listed by: OMICtools has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01454 | SCR_004850 | SciCrunch Registry | Metagenomic AND rDNA Taxonomic Assignment | 2026-10-10 12:37:03 | 26 | |||||||
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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 | SciCrunch Registry | MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences | 2026-10-10 12:37:06 | 11 | ||||||
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NucPosSimulator Resource Report Resource Website 1+ mentions |
NucPosSimulator (RRID:SCR_004765) | NucPosSimulator | software resource | A simulation tool to identify positions of nucleosomes from Next Generation Sequencing data. |
is listed by: OMICtools has parent organization: University of Applied Sciences; Mecklenburg-Vorpommern; Germany |
BMBF | PMID:23846748 | Acknowledgement requested, Free, Public | OMICS_00512 | SCR_004765 | SciCrunch Registry | 2026-10-10 12:37:05 | 5 | |||||||
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MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | data analysis resource, data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes. | microbial community, microbial composition, microbial genome, microbial sequence |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: Bitbucket has parent organization: Harvard T.H. Chan School of Public Health |
PMID:22688413 DOI:10.1038/nmeth.3589 |
OMICS_02286 | http://huttenhower.sph.harvard.edu/metaphlan https://bitbucket.org/nsegata/metaphlan/, https://sources.debian.org/src/metaphlan2/ | SCR_004915 | SciCrunch Registry | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-10-10 12:37:25 | 645 | |||||||
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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 | SciCrunch Registry | 2026-10-10 12:37:20 | 131 | ||||||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | SciCrunch Registry | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-10-10 12:36:55 | 17718 |
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