News and Changelogs
News
New paper on the TYGS and LPSN database tandem published in Nucleic Acids Research
2021-10-19
Our new paper describing the relationship between the databases of the Type (Strain) Genome Server (TYGS) and the List of Prokaryotic names with Standing in Nomenclature (LPSN) was recently published in Nucleic Acids Research:
Change
Increased retention time for user jobs from 2 weeks to 4 weeks
2021-04-14
As you might have noticed, the TYGS will remove old job results mainly due to data privacy reasons. The old job result lifetime was 2 weeks and was now extended to 4 weeks. Apart from that, whenever you need your job results a bit longer, just use the contact form to send us a short request and we will extend the lifetime of your job.
News
TYGS Year 2020 in Review report released in both PDF and PNG format
2021-02-22
Change
Faster javascript plugin for manual selection of type strain genomes
2021-02-21
[CHANGED] TYGS now uses a much faster and more convenient multi select javascript plugin called virtual-select.
Change
Reconstruction of proteome-based GBDP trees
2021-01-31
[ADDED] For very diverse datasets of strains, the average branch support, even of the genome-based phylogeny, might be too low which is not unlikely for such datasets. An optional proteome-based GBDP analysis will become available on user request if the dataset is not too large (< 30 strains) and the average branch support of the genome-based tree is smaller than 50%.
Change
Extended 16S rRNA gene sequence analysis now available from main TYGS result page
2021-01-31
[CHANGED] The extended SSU analysis will now be found on the main TYGS result page and not longer on the subpage of the 16S GBDP phylogeny.
News
Several milestones reached
2020-10-20
| ~7,000,000 | total number of pairwise genome comparisons |
| ~600,000 | average number of pairwise genome comparisons per month |
| >13,000 | total number of TYGS analyses so far |
| >2,000 | total number of distinct scientists from all around the world so far |
| ~300 | average number of distinct scientists per month |
| ~130 | average number of first-time users per month |
Change
GBDP core
2020-08-12
[CHANGED] A routine was replaced in the coverage algorithm of the GBDP core, with the newer one being a bit more complex but better able to deal with highly similar genome sequences that significantly differ in length and are highly redundant e.g. due to sequencing or assembly artifacts.
Change
Splitting of user requests
2020-06-13
[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.