I am trying to do some phylogenetic analysis on a family of bacterial transporters, but keep getting this strange tree with one group that is basically the root (i.e. the branch length is almost 0)(see top left part of circle). So far I've tried using RaxML, PhyML and MrBayes and they've all given me the same thing, but with different groups at the "root", which is even more troubling.
Has anyone encountered such a problem before? Is this more likely to just be a limitation of the method, or does it actually suggest something important about the evolutionary relationships? Would greatly appreciate any ideas, opinions and recommendations (alternative methods etc)! My sequences are extremely similar so that could be a possible reason for this.