From the tree that i have I wanted to remove one of the nodes. is it possible to remove that node from the tree file?
No, it is impossible. If you want to remove any node, you should remove your particular sequence data from the mega file.
you can use Dendroscope software... click on the taxon of your interest and press DEL.
It is possible but the problem is disorganizing of your logical tree... It is not scientific but executable
Although technically possible (depending on the software you are using), it is not recommended in general, because every sequence was used to compute the clustering of your nodes. Therefore, removing one and recalculating might lead to a different tree, and that is something that you will miss if you simply remove a node.
In short, remove the sequence/node only if you are completely sure that your tree is not going change very much (for example in cases of highly similar sequences); but if not, then recalculate your tree after you remove your sequence/node.
Best regards.
This software can be used to remove a node, among other phylogenetic tasks:
http://bosque.udec.cl/software/bosque.html
I tried using R employing ape package for removing the node. I got the message that the particular tip is removed but I am unable to view the modified tree. the taxa I want to remove is an obvious outlier occurring in all my trees and removing it will not change my tree topology. so I want to remove it. kindly folow the link attached
https://www.biostars.org/p/74459/#233893
I agree that it's not possible, as will disturb the proportions of the tree. I would then suggest to re-create the tree, as the safest solution.
You have to redo the analysis without the OTU, ESPECIALLY it if is an outlier, since strongly aberrant sequence data will influence the entire tree construct. NEVER just remove the OTU manually from the tree, although technically it is very easy to do: you open the tree file in a word editor and just delete the name string, the two associated parenthesis, and the comma. Of course the tricky aspect is to identify the correct associated parentheses.
It is posible
Example
R
> library(ape)
> library(geiger)
>getwd()
>list.files (getwd())
>Read.tree("Namefile.tre")
>my.phylocladeA = c("TaxaName", TaxaName2")
>culledtree
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