# Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?

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?

• 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).
– M__
May 23 '20 at 6:09
• 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. May 24 '20 at 7:20

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
• There are 30000 sequences.
– user8708
May 28 '20 at 18:54