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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?

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    $\begingroup$ 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). $\endgroup$
    – M__
    May 23 '20 at 6:09
  • $\begingroup$ 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. $\endgroup$
    – Shadi
    May 24 '20 at 7:20
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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
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  • $\begingroup$ There are 30000 sequences. $\endgroup$
    – user8708
    May 28 '20 at 18:54

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