Frequently Asked Questions FAQ

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Use of this form is free for academic purposes. For all other uses, please contact the authors.

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Browsing the TYGS web page is free and does not require registration.

For submitting a TYGS job, an e-mail address has to be provided along with some genome sequences and/or GenBank accession IDs, the subject of the subsequent analysis. The e-mail address is the only piece of person-related information stored by the TYGS. All data associated with a TYGS job, including the e-mail address, are deleted after the job has finished and an additional amount of time has passed. The exact time of deletion is indicated in the notification e-mail and in the information badges in the top-right corner of the TYGS result page.

Additional information is found in the general privacy statement of the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, in accordance with the General Data Protection Regulation.

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Please see the GGDC/VICTOR FAQ for detailed instructions on how to specify accession numbers.

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Please see the GGDC/VICTOR FAQ for detailed explanations of why an e-mail may get lost. Also note that the TYGS results are additionally displayed on a website.

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While the TYGS database attempts to be as comprehensive as possible, a specific type-strain genome may be missing for a variety of reasons:

• The genome has not yet been sequenced.
• The genome sequence has been obtained but not been deposited in public databases.
• The genome sequence has been deposited in public databases but cannot be identified because its metadata lack crucial information.
• The genome sequence has been deposited in public databases but cannot be identified because a deposit of the type strain was used that is unknown to the TYGS database.
• The genome sequence can be identified in public databases but fails the TYGS quality checks.

If you are aware of a type-strain genome sequence that is missing in the TYGS database, please contact the maintainers and provide information on this genome sequence as indicated above.

Prior to sending a report on a missing type-strain genome sequence, make sure the species or subspecies is not contained in the list for manual genome selection. If it is contained, you may better file a report on a type-strain genome sequence that is contained but not automatically found.

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Click on the refresh symbol close to "Click to load or refresh tree (page needs to be viewed in https session)" on the tree page.

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In addition to the routine import of taxonomic and genomic information, the following user-visible changes were applied to the database after the initial Nature Communications publication:

2019-07-23

Type(-strain) reference genome sequences with >500 contigs are accepted if the annotation contains a 16S rRNA gene sequence. When introduced this change resulted in the addition of only few dozens of new genome sequences.

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The TYGS has a basic API for the programmatic download of results:

1 Literature download:

2 Download of trees in Newick format:

3 Download of trees in PhyloXML format:

Note: we will add more download options for other types of results in the future (e.g. TYGS result Tables 2 and 3).