The whole paragraph has been deleted. This paragraph was added to the revised manuscript because one of the Reviewers asked “Does CVTree still require input genome data to be annotated to gene features, i.e., protein or CDS?” Well, this question reminds us that for many so-called “Permanent Draft” genomes it may be worthwhile returning to our early practice of using whole genome nucleotide sequences without distinguishing coding and non-coding segments. Although it did not lead to better results as compared with using translated protein products, but it is doable on un-annotated contigs. We will try this later.
L81–85: I think this paragraph is interrupting a bit the text flow. I suggest deletion.