Hi everyone!

I was given a task to build a phylogenetic tree from a list of very diverse proteomes. I don't have much experience in this field, so I have read some articles and decided to use non-alignment FFP method and follow methodology described here and here.

They are using shuffled genomes of real organisms as an outgroop for tree rooting but i cannot find any description how to do the genome shuffling properly. I tried to download multifasta of some random proteome and then shuffle randomly every amino acid sequence separately. I am using this proteome.

My tree looks basically like this:

   /-outgroop
  |
--|   /-methanocaldococcus
  |  |
  |  |   /-escherichia
   \-|  |
      \-|  
        |  
         \- eucaryotes - they seem fine

That methanocaldococcus is archean so I would guess it should be closer to the eucaryotes than e. coli. Can it be that I messed up with the outgroup, and now it is attracting the archean sequence? Should I do the genome shuffling differently or should I choose genome for the outgroup in a different way?

Thanks for all answers.