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.
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Is there a way in R to make sure that all nodes are presented in the phylogenetic tree?
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
Appreciate if anyone can help with this. Here is the Newick file that I use.