Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-25T17:47:37.647Z
Answers.Text: Thanks for inquiring. Too bad that their response doesn't contain more details or a link to the pipeline. Seems like they calculate the average PID of all alignments reported by blastn und use that as a distance measure. I wonder if they also consider the parts of each genome pair that are not covered by alignments.
Answers.UserDisplayName: Peter Menzel
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-24T14:28:40.923Z
Answers.LastActivityDate: 2018-10-24T14:28:40.923Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: Kohl Kinning
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-28T00:16:27.167Z
Comments.Text: They say "based on genomic BLAST". No useful information can be found, though.
Comments.UserDisplayName: user172818
Tags: <phylogenetics><genbank>
Title: Source for whole genome comparisons at NCBI Genomes
ThreadText: # Source for whole genome comparisons at NCBI Genomes
  
  (Asked by: username_0 on 2018-09-27)
  
  The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. [Pseudonomas aeruginosa](https://www.ncbi.nlm.nih.gov/genome/?term=txid208964[Organism:exp]) or [Escherichia coli](https://www.ncbi.nlm.nih.gov/genome/167).
  
  How were these comparisons done? Someone knows the source / paper?
  
  **Tags:** phylogenetics, genbank
  
  > **Comments:**
  > **username_1**: They say "based on genomic BLAST". No useful information can be found, though.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2018-10-24. Score: 1 | Accepted answer
  
  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*
  
  > **Comments:**
  > **username_0**: Thanks for inquiring. Too bad that their response doesn't contain more details or a link to the pipeline. Seems like they calculate the average PID of all alignments reported by blastn und use that as a distance measure. I wonder if they also consider the parts of each genome pair that are not covered by alignments.  
  
  ---
  
  