<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>

CC BY-SA 4.0
2020-05-24T07:59:26.250Z
2020-05-24T07:59:26.250Z
M__
<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>

CC BY-SA 4.0
2020-05-23T06:09:05.623Z
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__
CC BY-SA 4.0
2020-05-24T07:20:43.447Z
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.
Shadi
<phylogeny><covid-19><sars-cov-2><genbank>
Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?
# 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 @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).  
> **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.  

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## 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


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