[ADDED] Sometimes job submissions contain user genomes or metagenomic bins that are only remotely related, if at all. But a single TYGS analysis including all of these genomes at once would then result in a 'bloated' user request analysis when being subjected to the automatic determination of closest type strain neighbors. In such cases the TYGS now splits your request into two or more sub requests reflecting groups of genomic relatedness. the job confirmation page now also holds an overview of the status of these forked requests and a direct link to the individual result pages. This feature further improves your genome-based taxonomic analyses by finding an even more suitable type strain selection.
News
Preferred names of type strains now link to the rebooted LPSN page
2020-02-12
Since February 2020 the LPSN page (List of Prokaryotic names with Standing in Nomenclature) is now officially hosted, developed and maintained at the Leibniz Institute DSMZ and readily available under https://lpsn.dsmz.de. This affects the TYGS in so far as the preferred name of each type strain listed in Table 4 of your individual TYGS result page now links to the specific LPSN page of that species. Moreover, links to the BacDive database now go to the specific strain page whenever possible.
Change
Compact PDF report of your individual TYGS result page
2019-12-12
[ADDED] Since December 2019 the TYGS also offers the download of a nice publication-ready PDF report which can, in principle, be added to a paper as a supplement.
Change
Genome-based approach to determine closest type strain genomes
2019-10-30
[CHANGED] The most closely related type-strain genomes are now also determined independently of 16S rRNA gene sequences. In addition to the ten closest type-strain genomes determined via the smallest 16S rRNA sequence distances, the TYGS now also calculates intergenomic MASH distances (PubMed ID: 27323842), a fast approximation of intergenomic relatedness, between each uploaded genome sequence and the entire set of type strain genomes contained in the TYGS database. The set of type-strain genomes with the smallest MASH distances is combined with those having the smallest 16S rRNA gene distances. This approach ensures that even if the user genome sequence does not contain a 16S rRNA gene and even in organismal groups in which the 16S rRNA gene sequence does not well resolve the pairwise relationships, the most closely related type strains are chosen. Note that the usage of 16S rRNA gene sequences remains relevant for detecting closely related type strains that have not yet been genome-sequenced.
Change
Tree export to PNG format
2019-08-27
[FIXED] The legend text is no longer cut off at the top when exporting trees to PNG format.
Change
Quality criteria for the import of reference genomes
2019-07-23
[CHANGED] New type(-strain) reference genome sequences are only included in the TYGS database, if certain quality criteria are met. The latter were recently adjusted, i.e., now genomes 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.