Question: Weird phylogenetic tree (bacterial transporters)
gravatar for gpng
3.8 years ago by
gpng0 wrote:

enter image description here


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.

Thank you!

ADD COMMENTlink written 3.8 years ago by gpng0

Are the short branches maybe highly similar sequences, if they are, this might result in close to 0 substitutions per site.

ADD REPLYlink written 3.8 years ago by Michael Dondrup47k

Are you specifying the root explicitly? Be aware that some visualizers select the root taxon arbitrarily. Do things look okay when you visualize the phylogeny as unrooted?

ADD REPLYlink written 3.8 years ago by Brice Sarver3.5k

Hi! Thanks for the reply. This is the unrooted tree.

ADD REPLYlink written 3.8 years ago by gpng0
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