DNA & microbial identification

Strain-level bacterial and archaeal taxonomy, morphology, physiology, cultivation, isolation, biosafety and sequence links, including type strains.

Best for

Checking whether a microbial candidate agrees with a documented strain's provenance, morphology, physiology and culture conditions.

Limits

Not a visual identification key. Culture-derived phenotypes can differ from environmental observations, uncultured diversity is underrepresented and record completeness varies.

Coverage

Global bacterial and archaeal strains held by culture collections and represented in the literature.

Reuse

CC BY 4.0 for BacDive data.

Contributing

Browsing is open; some programmatic services require free registration.

A cross-taxon platform joining standard barcode sequences to specimen, voucher, image, collection and taxonomy metadata with identification engines.

Best for

Matching an appropriate barcode marker against specimen-linked references and inspecting the evidence behind the closest records.

Limits

Coverage and label quality are uneven, private records can make a result hard to reproduce, and Barcode Index Numbers are operational clusters rather than formally described species.

Coverage

Global animals, plants, fungi and other groups using supported barcode loci.

Reuse

Record, sequence and media rights vary by contributor and project; check every reference record before reuse.

Contributing

Public search and identification are free. An account is required for workbench, project and submission functions.

General nucleotide and protein sequence-similarity searching across curated and broad public databases, with accession-level results.

Best for

Tracing a query to candidate accessions and publications when no more appropriate specialist identification service covers the marker.

Limits

Similarity is not identity. Broad databases contain submitter-supplied labels, contaminants and uneven curation, and no universal percentage threshold establishes a species.

Coverage

Global public nucleotide and protein sequence collections across all organisms.

Reuse

Public sequence records follow NCBI and source-database policies; cite accessions and the database searched.

Quality-controlled, aligned small- and large-subunit ribosomal RNA reference datasets with taxonomy, browsers and downloads.

Best for

Broad 16S, 18S, 23S or 28S placement using a release that can be recorded and reproduced.

Limits

Reference and Parc subsets have different curation levels; not every record is type-validated, eukaryotic curation is uneven and taxonomy changes between releases.

Coverage

Cellular life across bacterial, archaeal and eukaryotic ribosomal RNA loci.

Reuse

CC BY 4.0; cite SILVA and the exact release used.

Curated fungal nuclear ITS references, expert annotations, reference sequences and DOI-bearing Species Hypotheses with analysis-ready releases.

Best for

Fungal ITS assignment with a versioned reference set and operational hypotheses that can be cited precisely.

Limits

Species Hypotheses are threshold-dependent clusters rather than formal species. ITS resolution differs among clades and underlying public labels can still be imperfect.

Coverage

Global fungi and selected other eukaryotes represented by ITS sequences.

Reuse

CC BY for UNITE releases; retain the release DOI and attribution.

Contributing

Browsing and downloads are open; registration is used for advanced PlutoF curation tools.

An expert-curated 18S ribosomal RNA reference taxonomy for protists with downloadable releases and metabarcoding support.

Best for

Protist-specific 18S assignment using a curated taxonomic framework rather than a broad unfiltered sequence archive.

Limits

A sequence reference rather than morphology; 18S often cannot resolve species, environmental labels can be uncertain and expert coverage varies among clades.

Coverage

Global protists, with selected fungi, animals and plants retained for context.

Reuse

Open releases; cite PR² and record the database version used.

Strain-level bacterial and archaeal taxonomy, morphology, physiology, cultivation, isolation, biosafety and sequence links, including type strains.

Best for

Checking whether a microbial candidate agrees with a documented strain's provenance, morphology, physiology and culture conditions.

Limits

Not a visual identification key. Culture-derived phenotypes can differ from environmental observations, uncultured diversity is underrepresented and record completeness varies.

Coverage

Global bacterial and archaeal strains held by culture collections and represented in the literature.

Reuse

CC BY 4.0 for BacDive data.

Contributing

Browsing is open; some programmatic services require free registration.

Whole-genome identification and classification against type-strain genomes using digital DNA–DNA hybridisation, G+C comparison and phylogenomics.

Best for

Testing a bacterial or archaeal genome against type-strain references with a standards-oriented, documented workflow.

Limits

Requires a usable genome, can queue jobs and cannot compensate for missing or problematic type-genome data. Its result still needs sample and contamination scrutiny.

Coverage

Prokaryotic taxa with suitable type-strain genome references.

Reuse

DSMZ service terms apply; cite the TYGS method and references returned with the result.

Contributing

Submission is free and uses an email address to return results; no persistent user account is required.

A cross-taxon platform joining standard barcode sequences to specimen, voucher, image, collection and taxonomy metadata with identification engines.

Best for

Matching an appropriate barcode marker against specimen-linked references and inspecting the evidence behind the closest records.

Limits

Coverage and label quality are uneven, private records can make a result hard to reproduce, and Barcode Index Numbers are operational clusters rather than formally described species.

Coverage

Global animals, plants, fungi and other groups using supported barcode loci.

Reuse

Record, sequence and media rights vary by contributor and project; check every reference record before reuse.

Contributing

Public search and identification are free. An account is required for workbench, project and submission functions.

General nucleotide and protein sequence-similarity searching across curated and broad public databases, with accession-level results.

Best for

Tracing a query to candidate accessions and publications when no more appropriate specialist identification service covers the marker.

Limits

Similarity is not identity. Broad databases contain submitter-supplied labels, contaminants and uneven curation, and no universal percentage threshold establishes a species.

Coverage

Global public nucleotide and protein sequence collections across all organisms.

Reuse

Public sequence records follow NCBI and source-database policies; cite accessions and the database searched.

Quality-controlled, aligned small- and large-subunit ribosomal RNA reference datasets with taxonomy, browsers and downloads.

Best for

Broad 16S, 18S, 23S or 28S placement using a release that can be recorded and reproduced.

Limits

Reference and Parc subsets have different curation levels; not every record is type-validated, eukaryotic curation is uneven and taxonomy changes between releases.

Coverage

Cellular life across bacterial, archaeal and eukaryotic ribosomal RNA loci.

Reuse

CC BY 4.0; cite SILVA and the exact release used.

Curated fungal nuclear ITS references, expert annotations, reference sequences and DOI-bearing Species Hypotheses with analysis-ready releases.

Best for

Fungal ITS assignment with a versioned reference set and operational hypotheses that can be cited precisely.

Limits

Species Hypotheses are threshold-dependent clusters rather than formal species. ITS resolution differs among clades and underlying public labels can still be imperfect.

Coverage

Global fungi and selected other eukaryotes represented by ITS sequences.

Reuse

CC BY for UNITE releases; retain the release DOI and attribution.

Contributing

Browsing and downloads are open; registration is used for advanced PlutoF curation tools.

An expert-curated 18S ribosomal RNA reference taxonomy for protists with downloadable releases and metabarcoding support.

Best for

Protist-specific 18S assignment using a curated taxonomic framework rather than a broad unfiltered sequence archive.

Limits

A sequence reference rather than morphology; 18S often cannot resolve species, environmental labels can be uncertain and expert coverage varies among clades.

Coverage

Global protists, with selected fungi, animals and plants retained for context.

Reuse

Open releases; cite PR² and record the database version used.

Strain-level bacterial and archaeal taxonomy, morphology, physiology, cultivation, isolation, biosafety and sequence links, including type strains.

Best for

Checking whether a microbial candidate agrees with a documented strain's provenance, morphology, physiology and culture conditions.

Limits

Not a visual identification key. Culture-derived phenotypes can differ from environmental observations, uncultured diversity is underrepresented and record completeness varies.

Coverage

Global bacterial and archaeal strains held by culture collections and represented in the literature.

Reuse

CC BY 4.0 for BacDive data.

Contributing

Browsing is open; some programmatic services require free registration.

A reference for valid publication status, nomenclatural history, synonyms, type strains and literature under the prokaryotic nomenclature code.

Best for

Checking whether a bacterial or archaeal name is validly published and identifying its nomenclatural type strain.

Limits

Nomenclature is not identification and LPSN is not an official universal biological classification. A valid name says nothing about whether the query belongs to that taxon.

Coverage

Global names of Bacteria and Archaea governed by the International Code of Nomenclature of Prokaryotes.

Reuse

Attribution and DSMZ Digital Diversity terms apply; API and downloads require registration.

Whole-genome identification and classification against type-strain genomes using digital DNA–DNA hybridisation, G+C comparison and phylogenomics.

Best for

Testing a bacterial or archaeal genome against type-strain references with a standards-oriented, documented workflow.

Limits

Requires a usable genome, can queue jobs and cannot compensate for missing or problematic type-genome data. Its result still needs sample and contamination scrutiny.

Coverage

Prokaryotic taxa with suitable type-strain genome references.

Reuse

DSMZ service terms apply; cite the TYGS method and references returned with the result.

Contributing

Submission is free and uses an email address to return results; no persistent user account is required.

A cross-taxon platform joining standard barcode sequences to specimen, voucher, image, collection and taxonomy metadata with identification engines.

Best for

Matching an appropriate barcode marker against specimen-linked references and inspecting the evidence behind the closest records.

Limits

Coverage and label quality are uneven, private records can make a result hard to reproduce, and Barcode Index Numbers are operational clusters rather than formally described species.

Coverage

Global animals, plants, fungi and other groups using supported barcode loci.

Reuse

Record, sequence and media rights vary by contributor and project; check every reference record before reuse.

Contributing

Public search and identification are free. An account is required for workbench, project and submission functions.

General nucleotide and protein sequence-similarity searching across curated and broad public databases, with accession-level results.

Best for

Tracing a query to candidate accessions and publications when no more appropriate specialist identification service covers the marker.

Limits

Similarity is not identity. Broad databases contain submitter-supplied labels, contaminants and uneven curation, and no universal percentage threshold establishes a species.

Coverage

Global public nucleotide and protein sequence collections across all organisms.

Reuse

Public sequence records follow NCBI and source-database policies; cite accessions and the database searched.

Quality-controlled, aligned small- and large-subunit ribosomal RNA reference datasets with taxonomy, browsers and downloads.

Best for

Broad 16S, 18S, 23S or 28S placement using a release that can be recorded and reproduced.

Limits

Reference and Parc subsets have different curation levels; not every record is type-validated, eukaryotic curation is uneven and taxonomy changes between releases.

Coverage

Cellular life across bacterial, archaeal and eukaryotic ribosomal RNA loci.

Reuse

CC BY 4.0; cite SILVA and the exact release used.

Curated fungal nuclear ITS references, expert annotations, reference sequences and DOI-bearing Species Hypotheses with analysis-ready releases.

Best for

Fungal ITS assignment with a versioned reference set and operational hypotheses that can be cited precisely.

Limits

Species Hypotheses are threshold-dependent clusters rather than formal species. ITS resolution differs among clades and underlying public labels can still be imperfect.

Coverage

Global fungi and selected other eukaryotes represented by ITS sequences.

Reuse

CC BY for UNITE releases; retain the release DOI and attribution.

Contributing

Browsing and downloads are open; registration is used for advanced PlutoF curation tools.

An expert-curated 18S ribosomal RNA reference taxonomy for protists with downloadable releases and metabarcoding support.

Best for

Protist-specific 18S assignment using a curated taxonomic framework rather than a broad unfiltered sequence archive.

Limits

A sequence reference rather than morphology; 18S often cannot resolve species, environmental labels can be uncertain and expert coverage varies among clades.

Coverage

Global protists, with selected fungi, animals and plants retained for context.

Reuse

Open releases; cite PR² and record the database version used.

Strain-level bacterial and archaeal taxonomy, morphology, physiology, cultivation, isolation, biosafety and sequence links, including type strains.

Best for

Checking whether a microbial candidate agrees with a documented strain's provenance, morphology, physiology and culture conditions.

Limits

Not a visual identification key. Culture-derived phenotypes can differ from environmental observations, uncultured diversity is underrepresented and record completeness varies.

Coverage

Global bacterial and archaeal strains held by culture collections and represented in the literature.

Reuse

CC BY 4.0 for BacDive data.

Contributing

Browsing is open; some programmatic services require free registration.

A reference for valid publication status, nomenclatural history, synonyms, type strains and literature under the prokaryotic nomenclature code.

Best for

Checking whether a bacterial or archaeal name is validly published and identifying its nomenclatural type strain.

Limits

Nomenclature is not identification and LPSN is not an official universal biological classification. A valid name says nothing about whether the query belongs to that taxon.

Coverage

Global names of Bacteria and Archaea governed by the International Code of Nomenclature of Prokaryotes.

Reuse

Attribution and DSMZ Digital Diversity terms apply; API and downloads require registration.