hello Lina

you can create phylogenetic tree from NCBI blast and click on Distance tree of results and you can download your file in many formats

Yes, of course its correct (about reference data - https://bacterio.net/ is the best for comparison with type strains). I can recomend MEGA or UNIPRO Ugene packages for your purpouse - they are easy to use and work in any OS, just download all analysing sequences to text file and work with them as it describe in the manual

Although people who answer to the question interpreted the question and answered it accordingly, however, the way this question was asked is wrong.

• Accession numbers are nothing but just an identity of the sequence, which does not have any relevance in the phylogentic tree construction
• phylogentic tree is constucted with the sequence data (nucleotide or protein) with 3 or more sequences
• However, the last point in which you are presenting your idea, is correct.