Frequently Asked Questions FAQ

Answer

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

"Academic purposes" do not include running queries just to collect and potentially plagiarize the type-strain genomes and other associated meta data included in the TYGS database. If you are unsure if and how to properly use the TYGS, do not hesitate to contact the TYGS team via the contact form.

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 was identified in public databases but is still under investigation by the TYGS team.
• 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.

1 Get status of request:

2 Get identification results:

3 Get dDDH results:

4 Get strain table:

5 Literature download:

6 Download of trees in Newick format:

7 Download of trees in PhyloXML format:

Answer

For some species the TYGS database contains the genome sequences of more than one strain deposit (e.g. ATCC and DSM). Now, if a user-provided genome sequence results in a close match with such a species all strain deposits of that species are usually included in the TYGS result. The main reason is that the scientific literature reports rare cases in which such strains unexpectedly differ to a considerable extent thus indicating a strain confusion or contamination (please find an example here). That way, the TYGS is an important tool to uncover such irregularities.

Apart from that, we think that having more than one strain deposit of the same species included in the dataset is at most a cosmetic issue, not a scientific problem. If you still want to remove such "duplicates", you have the option to download the trees in Newick format and remove them. We however advise against post-manipulation of ready-made results.

Answer

The TYGS is showing such matches because it may be important for any taxonomist to be aware of all closely related species or subspecies even if their names are not (yet) validly published. Since several criteria have to be met before a new species name is validly published (see details on LPSN page), the entire process might take some time. For example, it can well be that a novel species or subspecies name was already proposed in an effective publication but has still not been announced in a Validation List. In theory, a second team might now start working on the description of the same taxon, resulting in redundant work. That is, if your novel strain is placed in the same species or subspecies cluster as a species or subspecies with a not (yet) validly published name, we recommend to get in touch with its authors. An effective publication may be available and the valid publication of the name may be imminent. And even in the case of a low probability of a forthcoming validation it is often worth reporting phylogenetically close relationships to taxa that lack a validly published name. Their names occur in databases anyway and their analyses may yield valuable information.