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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PathSeq Resource Report Resource Website 50+ mentions |
PathSeq (RRID:SCR_005203) | PathSeq | software resource | A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences. | virus, microbe, pathogen, dna, rna, next-generation sequencing |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Broad Institute |
PMID:21552235 | Acknowledgement requested, Account required, (for Amazon Web Services and you will need to pay for the AWS resource time) | OMICS_00221 | SCR_005203 | PathSeq: Pathogen Discovery | 2026-02-07 02:06:41 | 60 | ||||||
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CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | data or information resource, database | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-02-11 10:58:41 | 2045 | ||||||
|
MPIDB Resource Report Resource Website 1+ mentions |
MPIDB (RRID:SCR_001898) | MPIDB | data or information resource, database | Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included. | 3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiology |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Database of Interacting Proteins (DIP) is related to: BIND is related to: MINT is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry has parent organization: J. Craig Venter Institute |
J. Craig Venter Institute ; Indgen Life Technologies ; NIH ; NIMH R01GM79710 |
PMID:18556668 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10467 | http://jcvi.org/mpidb/ | SCR_001898 | The Microbial Protein Interaction Database, Microbial Protein Interaction Database | 2026-02-11 10:56:20 | 5 | ||||
|
Type-III-Secretion-System related database Resource Report Resource Website |
Type-III-Secretion-System related database (RRID:SCR_002941) | T3DB | data or information resource, database | Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes. | type iii secretion system, gene, protein, ortholog |
is listed by: OMICtools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:22545727 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05160 | SCR_002941 | T3SS-related Database | 2026-02-11 10:56:34 | 0 | ||||||
|
Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-02-11 10:56:45 | 4 | ||||
|
HOMD Resource Report Resource Website 100+ mentions |
HOMD (RRID:SCR_012770) | HOMD | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on April 14,2022. Database of comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to use tools for viewing all publicly available oral bacterial genomes. Data is also downloadable. | taxon, genome, 16s rna, sequence, actinobacteria, bacteroidetes, chlamydiae, chloroflexi, euryarchaeota, firmicutes, fusobacteria, proteobacteria, spirochaetes, sr1, synergistetes, tenericutes, tm7, nomenclature, naming scheme, human, FASEB list | has parent organization: Forsyth Institute | NIDCR ; ARRA ; DOE contract U01 DE016937; DOE DE016937; DOE DE015847; DOE DE017106 |
PMID:20624719 PMID:20656903 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22198 | SCR_012770 | Human Oral Microbiome Database | 2026-02-11 10:58:44 | 137 | |||||
|
SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | data or information resource, database | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva https://doi.org/10.17616/R3FP60 |
SCR_006423 | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-02-11 10:57:24 | 13429 | ||||||
|
Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-02-11 10:57:26 | 64 | |||
|
ProLysED - Prokaryotic Lysis Enzymes Database Resource Report Resource Website |
ProLysED - Prokaryotic Lysis Enzymes Database (RRID:SCR_007183) | ProLysED | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 14, 2014. Database on the subject of bacterial (prokaryotic) proteases. ProLysED is a freely browsable using the Demo account. Certain services will require user registration. | protease | has parent organization: National University of Malaysia; Selangor; Malaysia | PMID:16128617 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03344 | http://genome.ukm.my/prolyses/ | SCR_007183 | Prokaryotic Lysis Enzymes Database | 2026-02-11 10:57:32 | 0 | |||||
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EOL - Encyclopedia of Life Resource Report Resource Website 100+ mentions |
EOL - Encyclopedia of Life (RRID:SCR_005905) | EOL | data or information resource, portal, database | Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise. | life, encyclopedia, environmental sciences, ecology, ecological survey, life sciences, specie, species diversity, diversity, taxon, image, video, audio, FASEB list |
is listed by: re3data.org is related to: Pensoft is related to: Biodiversity Heritage Library |
John D. and Catherine T. MacArthur Foundation ; Alfred P. Sloan Foundation |
PMID:24891832 | Creative Commons License, Acknowledgement requested, Note that a single page may be made up of many different data elements, Each covered by a different license, Http://eol.org/info/copyright_and_linking#using_content | r3d100010229, nlx_149476 | https://doi.org/10.17616/R35S3D | SCR_005905 | Encyclopedia of Life | 2026-02-12 09:44:08 | 138 | ||||
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Integrative Human Microbiome Project Resource Report Resource Website 1+ mentions |
Integrative Human Microbiome Project (RRID:SCR_015586) | iHMP | data or information resource, portal, project portal | Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions. | human microbiota, human microbiome, microbiota repository, metagenomic data, metatranscriptomic data, human genetic data, microbial culture data |
is affiliated with: Stanford University; Stanford; California is affiliated with: Virginia Commonwealth University; Virginia; USA is affiliated with: Broad Institute is affiliated with: Jackson Laboratory is affiliated with: University of Maryland School of Medicine; Maryland; USA is related to: Human Microbiome Project |
PMID:25211071 | Free, Freely available | http://ihmpdcc.org/ | SCR_015586 | Integrative Human Microbiome Project (iHMP) | 2026-02-12 09:46:34 | 3 | ||||||
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ATCC Genome Portal Resource Report Resource Website 1+ mentions |
ATCC Genome Portal (RRID:SCR_021330) | data or information resource, portal, database | Comprehensive collection of high quality microbial genomics reference data for bacteria, viruses, and fungi in holdings of American Type Culture Collection. | Genomic Databases, Genomic Datasharing, Genome Database, Reference Genome Project, cell line authentication, Genomics, Microbial Genomics Database, Fungal Databases, Database, Collection, Culture Collection | Restricted | r3d100013727 | https://www.atcc.org/the-science/authentication/enhanced-authentication-initiative https://doi.org/10.17616/R31NJN33 |
SCR_021330 | 2026-02-12 09:47:18 | 8 | |||||||||
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BacMap: Bacterial Genome Atlas Resource Report Resource Website 1+ mentions |
BacMap: Bacterial Genome Atlas (RRID:SCR_006988) | BacMap | data or information resource, atlas, database | An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes. It uses a visualization tool (CGView) to generate high-resolution circular genome maps from sequence feature information. Each map includes an interface that allows the image to be expanded and rotated. In the default view, identified genes are drawn to scale and colored according to coding directions. When a region of interest is expanded, gene labels are displayed. Each label is hyperlinked to a custom ''gene card'' which provides several fields of information concerning the corresponding DNA and protein sequences. Each genome map is searchable via a local BLAST search and a gene name/synonym search. A complete listing of the species and strains in the BacMap database is available on the BacMap homepage. Below each species/strain name is a list of the sequenced chromosomes and plasmids that are available. Some features of BacMap include: * Maps are available for 2023 bacterial chromosomes. * Each map supports zooming and rotation. * Map gene labels are hyperlinked to detailed textual annotations. * Maps can be explored manually, or with the help of BacMap''s built in text search and BLAST search. * A written synopsis of each bacterial species is provided. * Several charts illustrating the proteomic and genomic characteristics of each chromosome are available. * Flat file versions of the BacMap gene annotations, gene sequences and protein sequences can be downloaded. BacMap can be used to: * Obtain basic genome statistics. * Visualize the genomic context of genes. * Search for orthologues and paralogues in a genome of interest. * Search for conserved operon structure. * Look for gene content differences between bacterial species. * Obtain pre-calculated annotations for bacterial genes of interest. | gene, gene annotation, gene sequence, genome, bacteria, chromosome, protein sequence | has parent organization: University of Alberta; Alberta; Canada | Alberta Science Research Authority ; Western Economic Diversification ; Genome Canada ; Genome Prairie ; Western Economic Diversification Canada |
PMID:15608206 | Free, Acknowledgement requested | nif-0000-02591, r3d100012724 | https://doi.org/10.17616/R35502 | SCR_006988 | BacMap: An Interactive Atlas for Exploring Bacterial Genomes, BacMap genome atlas | 2026-02-12 09:44:29 | 4 | ||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | data repository, storage service resource, data or information resource, service resource, database | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-02-13 10:54:56 | 53 | ||||
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JGI Genome Portal Resource Report Resource Website 500+ mentions |
JGI Genome Portal (RRID:SCR_002383) | data or information resource, organization portal, portal, department portal | Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. | gene, computation, genome, genomics, model organism, assembly, annotation, sequenced genome, metagenome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute is parent organization of: Takifugu rubripes Genome |
Department of Energy | PMID:24225321 PMID:22110030 |
nif-0000-21230, SCR_004706, OMICS_01654, biotools:jgi_genome_portal, nlx_69965 | http://genome.jgi-psf.org https://bio.tools/jgi_genome_portal |
http://genome.jgi-psf.org/ | SCR_002383 | JGI Genome Portal, DOE Joint Genome Institute Genome Portal | 2026-02-13 10:55:01 | 865 | |||||
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MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | 2026-02-13 10:55:11 | 3 | |||||||
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RIKEN BioResource Center Resource Report Resource Website 1000+ mentions |
RIKEN BioResource Center (RRID:SCR_003250) | BRC, RIKEN BRC | biomaterial supply resource, organism supplier, material resource | RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad. | RIN, Resource Information Network, experimental animal, experimental plant, cultured cell line, dna, animal, plant, cell line, genetic material, virus, gene, cultured cell, embryo, sperm, tissue, organ, seed, cell, recombinant host, bioresource, FASEB list, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: RIKEN Tsukuba Institute; Kansai; Japan is parent organization of: JCM works with: Cellosaurus works with: International Mouse Strain Resource |
PMID:19448331 PMID:34532769 |
Free, Freely available | nif-0000-31407 | SCR_003250 | RIKEN Tsukuba Institute RIKEN BioResource Center | 2026-02-13 10:55:12 | 2208 | ||||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | sequence analysis software, data processing software, data 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 |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-02-13 10:55:25 | 5 | |||||
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DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity Resource Report Resource Website |
DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity (RRID:SCR_008028) | DNAftB | image collection, portal, data or information resource, video resource, narrative resource, training material, topical portal | An animated primer on the basics of DNA, genes, and heredity organized around three key concepts: Classical Genetics, Molecules of Genetics, and Genetic Organization and Control. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links. | gene, genetic, chromosome, dna, heredity, human, protein, reverse transcriptase, transcription, translation, transposon, genetics, virus, rna, mutation | has parent organization: Cold Spring Harbor Laboratory | Josiah Macy Jr. Foundation | nif-0000-10208 | SCR_008028 | DNA from the Beginning | 2026-02-13 10:56:06 | 0 | |||||||
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MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | sequence analysis software, data processing software, data analysis resource, data 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 | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-02-13 10:55:32 | 637 |
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