Frequently Asked Question FAQ

Table 3 of the TYGS result page contains the pairwise dDDH values between your user genomes and the selected type-strain genomes. The dDDH values are provided along with their confidence intervals (C.I.) for the three different GBDP (Genome BLAST Distance Phylogeny) formulas:

• formula d₀ (a.k.a. GGDC formula 1): length of all HSPs divided by total genome length
• formula d₄ (a.k.a. GGDC formula 2): sum of all identities found in HSPs divided by overall HSP length
• formula d₆ (a.k.a. GGDC formula 3): sum of all identities found in HSPs divided by total genome length

While formulae d₀ and d₆ reflect the (dis-)similarity of the underlying genomes in terms of gene-content, formula d₄ reflects the proportion of sequence identity within the homologous parts of the underlying genomes. Moreover, formula d₄ is independent of genome length and is thus robust against the use of incomplete draft genomes.

More info on these formulas and the underlying GBDP method is found in the literature.