I have about 600 taxon represented in a circle phylogenetic tree based on gene sequences. I am using MEGA software. It was aligned with ClustalW and I ran a NJ tree with 100 bootstrap. I changed the view to circle format. I had bootstrapping values ranging from 1-99. When I select "topology only" in the menu, I find that some nodes show a bootstrapping value of 624, quite a few actually. When I turn off topology view, all nodes have <100 value. Could topology view be merging nodes? I only gave it 100 bootstrap when computing the NJ tree.
Thanks in advance.