text: user1802: The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. Pseudonomas aeruginosa  or Escherichia coli.
  How were these comparisons done? Someone knows the source / paper?
  
  user181: I inquired into the details of the dendrograms after becoming frustrated with the lack of information. As with Ensembl, I'm sure that the folks at NCBI have a standardized pipeline that they run the sequences through to generate these dendrograms as no specific source deserving attribution was mentioned:
  
  The tree is based on a pairwise, BLAST comparison of chromosome sequences (an assembly is used for genomes with 2 or more chromosomes). BLAST identity is normalized on sequence length. The distance map is generated by a Neighbor Joining algorithm, where the distance is the blast score.
  Dr. Wayne Matten, NCBI
  
  
original_text: 1802: <p>The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. <a href="https://www.ncbi.nlm.nih.gov/genome/?term=txid208964[Organism:exp]" rel="nofollow noreferrer">Pseudonomas aeruginosa</a>  or <a href="https://www.ncbi.nlm.nih.gov/genome/167" rel="nofollow noreferrer">Escherichia coli</a>.</p>
  
  <p>How were these comparisons done? Someone knows the source / paper?</p>
   181: <p>I inquired into the details of the dendrograms after becoming frustrated with the lack of information. As with Ensembl, I'm sure that the folks at NCBI have a standardized pipeline that they run the sequences through to generate these dendrograms as no specific source deserving attribution was mentioned:</p>
  <blockquote>
  <p>The tree is based on a pairwise, BLAST comparison of chromosome sequences (an assembly is used for genomes with 2 or more chromosomes). BLAST identity is normalized on sequence length. The distance map is generated by a Neighbor Joining algorithm, where the distance is the blast score.</p>
  <p><em>Dr. Wayne Matten, NCBI</em></p>
  </blockquote>
  