Standard for when to collapse phylogenetically uninformative nodes
If 1E6 is genetic distance, this means one nucleotide difference per million base pairs, which is of course incredibly small and bootstrapping at this level doesn't really work. So what I suspect is happening is that the bootstrap is so low it is not present on the tree. You can assign a cut-off bootstrap but anything below 75% is not interpretable in any case. What might be happening is you are producing the bootstrap &quot;cladogram&quot; which is showing a default branch length, but when &lt;1E6 genetic distance it is showing a trifurcation. This simply means the bootstrap of the consensus tree is so low it is collapsing the branch and this is a function of the very small genetic distance at this node.

Looking at your treefile I don't see any collapsed clades.
(Group_9:0.00000100000050002909,(Group_50:0.00507659947127924935, (.

The clade above has not been colapsed it is just a very small distance in a paraphyletic group. It looks fine to me, i.e. Group_9 is 1E6. It could look 'collapsed' simply because it is so small it is difficult to see. I hope thats ok?