**3.1. Clades and species**

**Figure 4.** *Klebsiella pneumonia* clade contains 534 full genome assemblies organized in 25 closely related genomic groups. Blue circles at the end of the branch represent a single genome; green boxes represent a group of genomes with

the box size proportional to the number of genomes.

238 Next Generation Sequencing - Advances, Applications and Challenges

**Figure 5.** Clade growth in four sequential snapshots.

Using a taxonomy-aware clustering algorithm does not completely solve the discrepancies between the species-level clades and traditional species. Genome sequences provide great opportunity to refine the classical taxonomic description of prokaryotes [23]. All cases of discrepancy were manually evaluated; most of them have been resolved by literature support. Some examples are described below.
