Source for whole genome comparisons at NCBI Genomes
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