thank you for the development and maintenance of awesome software.
I am a beginner bioinformatician and I am tackling my first phylogenetic tree analysis task.
I wonder, what do the numbers in quoted internal node names mean?
They’re not recognized by most of soft as branch lengths, only as labels. What do they mean then?
The 0.999 is the non-parametric bootstrap support for the node. EBI has a nice explanation of these values: Confidence | Phylogenetics.
Just to follow up on Donovan’s comment - one issue is that a newick file allows different ways to store the bootstrap values and internal node names.
the ARB software environment does it like this:
whereas, the online tree display tool iTOL has opted for this format:
A tree with internal node IDs:
A, B, C : leaf names
INT1, INT2 : internal node IDs
0.1, 0.3 : branch lengths
90,98 : bootstrap values```
The next version of GTDB-Tk (should be released next week) will have a helper method to convert the default GTDB-Tk (ARB-style) Newick trees into the format required by iTOL.