A faithful prokaryotic phylogeny should be inferred from genomic data and phylogeny determines taxonomy. The ever-growing amount of sequenced genomes makes this approach feasible and practical. Whole-genome phylogeny must be based on alignment-free methodology and should be verified by direct comparison with taxonomy at all ranks from domains down to species. When the number of genomes goes into tens of thousands, the realization of the above program also presents technical challenges. The power of a long-tested Web Server named Composition Vector Tree (CVTree) will be demonstrated on examples from mega-classification of bacteria to high resolution at and below the species level.
Part of the book: Phylogenetics