HOW TO 'collapse' all branches in a tree that have a support below a given value

[romain....@gmail.com]

Dear all,

Using a fully resolved phylogenetic tree with branch support values, I would like to collapse (or 'remove' ... not sure what would be the most appropriate term here) all branches of this tree that have, lets say, a support below 70% of boot.

At the end, I would like to obtain a tree in which all of these weakly supported branches are replaced by polytomies. 

Does anyone know a function in the ETE package that would allow me to do such thing ?

Thanks in advance for your help !

Romain

[Alexandros Pittis]

Hey Romain,

so, if I understand well, what you want is deleting lowly supported branches and making a polytomy instead. By deleting the corresponding node, the nodes below are by default transferred to the parental one, one "up". For instance :

from ete2 import Tree

t = Tree('(((a:1,b:1)1:1,c:1)1:1,((e:1,f:1)0.5:1,g:1)1:1);')

print t.get_ascii(attributes=['support', 'name'])

               /-1.0, a
          /1.0,
     /1.0,     \-1.0, b
    |    |
    |     \-1.0, c
-1.0,
    |          /-1.0, e
    |     /0.5,
     \1.0,     \-1.0, f
         |
          \-1.0, g

# Loop through the nodes below the basal one and delete based on their support attribute or any other condition.

for node in t.get_descendants():
    if not node.is_leaf() and node.support <= 0.7:
        node.delete()

print t.get_ascii(attributes=['support', 'name'])

               /-1.0, a
          /1.0,
     /1.0,     \-1.0, b
    |    |
    |     \-1.0, c
-1.0,
    |     /-1.0, g
    |    |
     \1.0, -1.0, e
         |
          \-1.0, f

Check the delete function and here for more examples on various operations.

Cheers,

Alexandros

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--

Alexandros Pittis, PhD candidate
Comparative Genomics Group

Centre for Genomic Regulation (CRG)
Barcelona Biomedical Research Park (PRBB)
Doctor Aiguader, 88
08003 Barcelona, Spain
alexandr...@crg.eu
http://gabaldonlab.crg.es

[romain....@gmail.com]

Hy Alex,

thanks a lot, that works perfectly !!

cheers,

Romain

[bioBalls]

Thank you very much!!!

Works perfect!

Greetings,
Armin

[Philip Ashton]

This was really useful, thanks!