The pragmatic species concept for Bacteria and
Archaea is ultimately based on DNA-DNA hybridization (DDH), a method known to
be tedious. The GGDC is a state-of-the-art
Virus taxonomy should be strongly informed by sequence-based methods. The web service VICTOR compares phages using their genome or proteome sequences. Results include phylogenomic trees with branch support and suggestions for the classification at the species, genus and family level.
A service which (i) infers maximum-likelihood and maximum-parsimony phylogenies using state-of-the-art methods and (ii) calculates exact pairwise similarities between gene sequences under settings qualifying for the application of phylum-specific 16S similarity thresholds.
GGDC yielded higher correlations with wet-lab DDH
(without mimicking its pitfalls) than other
The Genome BLAST Distance Phylogeny (GBDP) approach for calculating accurate intergenomic distances, the core of the GGDC, was originally developed to infer genome-based phylogenies. Its latest version allows for the inference of branch support and this has been successfully utilized in a number of important studies.
In contrast to DDH dissimilarities, differences in percent genomic G+C content between distinct species can be quite close to zero. They just cannot be larger than 1 within the same species (Meier-Kolthoff et al. 2014). Here, the GGDC helps users to easily obtain this information and to use it for species description.