Extract monophyletic subtree with ETE3 toolkit
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7 months ago

Hello,

I have a tree with duplication. I need to extract a subtree that is monophyletic to get orthologs. I have to following tree:

t2 = PhyloTree("((RED_18455.t1:0.00147625,(YEL_2874.t1:0.0138986,YEL_23839.t1:0.0506878)n2:0.00563198)n1:0.000294125,BLU_7991.t1:0.00203445)n0;", format=1)
print(t2)
      /-RED_18455.t1
   /-|
  |  |   /-YEL_2874.t1
--|   \-|
  |      \-YEL_23839.t1
  |
   \-BLU_7991.t1
  
R = t2.get_midpoint_outgroup()
t2.set_outgroup(R)
print(t2)
  /-YEL_23839.t1
--|
  |   /-YEL_2874.t1
   \-|
     |   /-RED_18455.t1
      \-|
         \-BLU_7991.t1
  
t2.set_species_naming_function(lambda node: node.name.split("_")[0])
print(t2.get_species)

{'RED', 'BLU', 'YEL'}

for node in t2.split_by_dups():
    print(node)
--YEL_23839.t1

   /-YEL_2874.t1
--|
  |   /-RED_18455.t1
   \-|
      \-BLU_7991.t1
  

As you can see, there are two subtrees. How can I pick the second subtree that has all three species represented once? or extract a single copy orthogroup from this?

Thanks.

ETE3 python3 • 167 views
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