The latter can be assigned only after comparison with a reference taxonomy which is not a rigid framework but a modifiable system. Though a dissimilarity measure figures in the CVTree algorithm, it is not realistic to delineate taxa by using this measure at least for the time being. Even if defined in the future, it must be lineage-dependent. For example, it cannot be expected that the same degree of dissimilarity may be used to delineate classes in all phyla. In addition, monophyly is a guiding principle in comparing branching order with taxonomy. Here monophyly must be understood in a pragmatic way restricted to the given set of input data and the reference taxonomy. If all genomes from a taxon appear exclusively in a tree branch, the branch is said to be monophyletic.” R6 One cannot tell the rank of a node/leaf in a tree by simply looking at it. A reference taxonomy is alwys needed. We put the following in the “Material and Method” section to explain it: “Branching order in a tree by itself does not bring about taxonomic ranks, e,g, class or order.
Authors emend classification of some strains.