Source for whole genome comparisons at NCBI Genomes 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?
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