Answer

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

Answer

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.

Answer

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

Answer

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.

Answer

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.

Answer

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.

Answer

In addition to the routine import of taxonomic and genomic information, the user-visible changes that were applied to the database after the initial Nature Communications publication are listed on the News and Changelogs page.

Answer

Yes, the TYGS has an API for the programmatic download of results:

BEFORE YOU START USING THE API: Please note that the underlying computing resources are limited. That is, please do not write scripts that run large-scale analyses via the TYGS by splitting larger datasets into chunks that comply with the current upload cap (i.e. please avoid "request bombing"). That way, you would block resources other users would want to use as well. If you want to run large-scale TYGS analyses, please contact the TYGS team. Whenever possible and deemed reasonable, we frequently offer to run large-scale analyses as part of a scientific collaboration - just ask. If you establish a script-based access to the TYGS, please use the TYGS resources in a considerate way, i.e., do not query the API a dozen of times a minute but rather check the status of your jobs only once or twice an hour. The best way would be to wait for the automated response email which is delivered upon finalization of your request.

The following API call will return the status of your job in JSON format. Once the finalization_date is set, the job is done.

https://tygs.dsmz.de/user_requests/show/status/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the identification results of your job (Table 2) in JSON format:

https://tygs.dsmz.de/user_results/show/identification_table_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the dDDH results of your job (Table 3) in JSON format:

https://tygs.dsmz.de/user_results/show/digital_ddh_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

The following API call will return the strain table of your job (Table 4) in JSON format:

https://tygs.dsmz.de/user_results/show/strain_table_json/<GUID>

'<GUID>' has to be replaced by the respective TYGS request guid.

Example

Download of literature (i.e., original species descriptions of the type strains included in a particular TYGS job) in BibTex format ...

... with species names italicized via LaTeX formatting commands:

https://tygs.dsmz.de/user_results/show/bibtex/<GUID>

Example

... with species names italicized via HTML formatting commands:

https://tygs.dsmz.de/user_results/show/bibtex_with_html/<GUID>

Example

In both cases '<GUID>' has to be replaced by the respective TYGS request guid.

Download of trees (either based on 16S rRNA gene sequence or genome-scale data):

16S tree in Newick format:

https://tygs.dsmz.de/user_phylogenies/16S/newick_by_guid/<GUID>

Example

Genome-scale tree in Newick format:

https://tygs.dsmz.de/user_phylogenies/genome/newick_by_guid/<GUID>

Example

In all cases '<GUID>' has to be replaced by the respective TYGS request guid.

Download of trees (either based on 16S rRNA gene sequence or genome-scale data):

16S tree in PhyloXML format:

https://tygs.dsmz.de/user_phylogenies/16S/phyloxmlannot_by_guid/<GUID>

Example

Genome-scale tree in PhyloXML format

https://tygs.dsmz.de/user_phylogenies/genome/phyloxmlannot_by_guid/<GUID>

Example

In all cases '<GUID>' has to be replaced by the respective TYGS request guid.