Answers.Body: <p>Okay, I'll provide a formal answer, Genbank phylogeny is to get a gist of the diversity. It isn't a formal phylogenetic analysis. You can down the tree as a pdf, I don't think you can download the treefile (in fact I'm pretty certain you can't). Genbank will perform a reasonable distance method and from recollection it will "collapse clades", so if you see little triangles on the tree it represents a large number of taxa represented as a triangle. </p>
  
  <p>I was surprised to learn there are 4000 SARS-CoV-2 sequences. </p>
  
  <p>To make a tree you need to download the data, align (muscle) and send through a formal phylogeny program. If you think Genbank is okay, then try MegaX its very point and clicky. Generally, maximum likelihood phylogeny has returned to vogue for at least 1 decade now (previously Bayesian). However, the Beast package is a Bayesian analysis which is still going strong and the main tool now used in molecular dating. </p>
  
  <p>In summary, to perform a tree analysis beyond Genbank</p>
  
  <ul>
  <li>use the download option (there are two variants - the entire genome or the cut locus based on the query sequence)</li>
  <li>align using muscle or clustalo (muscle is really quick(</li>
  <li>perform a tree analysis using MEGA X, phylml, raxml or Beast depending on what you objectives are</li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-24T07:59:26.250Z
Answers.LastActivityDate: 2020-05-24T07:59:26.250Z
Answers.UserDisplayName: M__
Body: <p>I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank <a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&amp;VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049" rel="nofollow noreferrer">here</a>.</p>
  <p>When I click on <code>Build phylogenetic tree</code>, it only has 200 nodes.</p>
  <p>Is this expected? I was expecting to see 4000 nodes.</p>
  <p>Is it simply a displaying issue where only 200 sequences per page are revealed while browsing the list of sequences? Is there a way to get the tree for all 4000 sequences?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-23T06:09:05.623Z
Comments.Text: Hi @shadi, I would assume the NCBI tree building program is restricted to 200 taxa/nodes. Please note a "node" is different from a "taxon" (optimal taxonomic unit).
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-24T07:20:43.447Z
Comments.Text: Makes sense. Do you know if there's any option to export the full phylogenetic tree? I'm assuming that they restrict to 200 just because of the display limits.
Comments.UserDisplayName: Shadi
Tags: <phylogeny><covid-19><sars-cov-2><genbank>
Title: Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?
ThreadText: # Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?
  
  (Asked by: username_0 on 2020-05-23)
  
  I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank [here](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049).
  
  When I click on `Build phylogenetic tree`, it only has 200 nodes.
  
  Is this expected? I was expecting to see 4000 nodes.
  
  Is it simply a displaying issue where only 200 sequences per page are revealed while browsing the list of sequences? Is there a way to get the tree for all 4000 sequences?
  
  **Tags:** phylogeny, covid-19, sars-cov-2, genbank
  
  > **Comments:**
  > **username_1**: Hi @username_0, I would assume the NCBI tree building program is restricted to 200 taxa/nodes. Please note a "node" is different from a "taxon" (optimal taxonomic unit).  
  > **username_0**: Makes sense. Do you know if there's any option to export the full phylogenetic tree? I'm assuming that they restrict to 200 just because of the display limits.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-05-24. Score: 2 | Accepted answer
  
  Okay, I'll provide a formal answer, Genbank phylogeny is to get a gist of the diversity. It isn't a formal phylogenetic analysis. You can down the tree as a pdf, I don't think you can download the treefile (in fact I'm pretty certain you can't). Genbank will perform a reasonable distance method and from recollection it will "collapse clades", so if you see little triangles on the tree it represents a large number of taxa represented as a triangle.
  
  I was surprised to learn there are 4000 SARS-CoV-2 sequences.
  
  To make a tree you need to download the data, align (muscle) and send through a formal phylogeny program. If you think Genbank is okay, then try MegaX its very point and clicky. Generally, maximum likelihood phylogeny has returned to vogue for at least 1 decade now (previously Bayesian). However, the Beast package is a Bayesian analysis which is still going strong and the main tool now used in molecular dating.
  
  In summary, to perform a tree analysis beyond Genbank
  
  * use the download option (there are two variants - the entire genome or the cut locus based on the query sequence)
  * align using muscle or clustalo (muscle is really quick(
  * perform a tree analysis using MEGA X, phylml, raxml or Beast depending on what you objectives are
  
  
  ---
  
  