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Plot phylogenetic tree with all ancestor nodes

Hi everyone,

I am trying to generate a phylogenetic tree and I noticed that the tree produced using MEGA software and R (using ape package) is a bit different where one of the ancestor node is removed.

(Open image in new tab for full image)

Untitled

Is there a way in R to make sure that all nodes are presented in the phylogenetic tree?

Edit:

In MEGA, I used default settings for both alignment (Clustal) and phylogenetic tree (NJ). For the comparison, I used the Newick file generated from MEGA and use the codes below:

tr = read.tree("tree.nwk");
tr$edge.length=NULL;
plot(gettree,show.node.label = T,no.margin = T);

I doubt NULLing the edge.length affect the tree. Below is the other tree generated without tr$edge.length=NULL;

ff

Appreciate if anyone can help with this. Here is the Newick file that I use.

phylogenetic tree r ape
• 2,445 views • link
written by AfinaM • AfinaM

Hi, this is not informative. Write in details the algorithms and parameters you used for MEGA and R-ape (with code in the latter case), and ideally, you should supply an example dataset to make it reproducible.

• 0 views • link
written by lessismore lessismore

Hi, I have edited the post.

• 0 views • link
written by AfinaM • AfinaM

I've tried using both to generate and still couldn't manage to get that one ancestor node to show up. Are you familiar using these packages? Here is the Newick file that I'm experimenting with.

• 0 views • link
written by AfinaM • AfinaM

Please try uploading your file to ITOL and see if you get a different result (it's easy to use):

https://itol.embl.de/upload.cgi

Could you tell me the accession number of the ancestor node?

• 0 views • link
written by Fatima Fatima

From iTOL website, I still get the same phylogenetic tree as in R. Here is the Newick file that I used.

• 0 views • link
written by AfinaM • AfinaM

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