text: user9238: I have been creating phylogenetic trees using RAxML (using Boostrap + ML) and I end up with a bestTree file, outputted in newick format. When I open up the tree in FigTree, I notice that it collapses many of the internal nodes with small values (1 x 10-6). I am working on visualizing the trees using ETE, which when I render the tree includes these small breakpoints. I was wondering if there is a standard for when to collapse nodes that are considered phylogenetically uninformative that I can apply. Thank you for any help.
  
  user3848: 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 "cladogram" which is showing a default branch length, but when <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?
  
original_text: 9238: <p>I have been creating phylogenetic trees using RAxML (using Boostrap + ML) and I end up with a bestTree file, outputted in newick format. When I open up the tree in FigTree, I notice that it collapses many of the internal nodes with small values (1 x 10-6). I am working on visualizing the trees using ETE, which when I render the tree includes these small breakpoints. I was wondering if there is a standard for when to collapse nodes that are considered phylogenetically uninformative that I can apply. Thank you for any help.</p>
   3848: <p>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.</p>
  <hr />
  <p>Looking at your treefile I don't see any collapsed clades.</p>
  <pre><code>(Group_9:0.00000100000050002909,(Group_50:0.00507659947127924935, (.
  </code></pre>
  <p>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?</p>
  