text: user8908: I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here.
  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?
  
  user3848: 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
  
  
original_text: 8908: <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>
   3848: <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>
  