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How to get a Newick file that contains the internal node number

I am trying to visualize and annotate a phylogenetic tree (Newick format) with Ggtree. However, in order to color all the descendents of a respective node, the internal nodes have to be numbered, and I found an author that did something similar to what I want to do, but in his case when he creates a tree object, he gets the internal node number as "node.label" and I was wondering if designed his Newick file in a way that would allow him to have that node.label. If any of you knows of a tool or software I can use to include the internal node number in my Newick file. enter image description here

ggtree phylogeny tree
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updated by dthorbur dthorbur • written by Angels • Angels

I'm pretty sure ggtree automatically assigns node labels as numeric values when you read in a tree, though it has been a while since I've used it. Have you tried to read your newick tree into R as a ggtree object? You could them inspect the structure of the object using str() on the object, and even the geom_nodelab function to label the nodes so you can see the ones you are after.

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written by dthorbur dthorbur

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