reading in multiple trees

[August Guang]

Hi,

I have files with bootstrap tree samples from RAxML. I want to be able to read in the bootstrap file into ete3 and then compute RF distances between the bootstrap tree samples. The Tree function seems to only be able to read in 1 tree/file; is there a way to read in a file with multiple trees?

[Jaime Huerta Cepas]

Hi August, 

yes - if each bootstrapped tree is in one line, something like this should work:

from ete3 import Tree

tree_collection = []

for newick in open("Raxml.bootstrap_file"):

  tree_collection.append(Tree(newick))

Then you could compute RF among all trees loaded in the tree collection list as necessary. 

HTH

-jaime

On 13 February 2017 at 21:38, August Guang <august...@brown.edu> wrote:

Hi,

I have files with bootstrap tree samples from RAxML. I want to be able to read in the bootstrap file into ete3 and then compute RF distances between the bootstrap tree samples. The Tree function seems to only be able to read in 1 tree/file; is there a way to read in a file with multiple trees?

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