Question: Phylogenetics:How to Generate a binary newick tree from a list of species
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gravatar for View7
12 months ago by
View70
View70 wrote:

I have a list of species from which I would like to generate a collapsed binary newick tree. I have tried in ete3, but it does not work. (PhyloT has this feature, but cannot be used as it is not free anymore )

ex)

poly_1 = Test_tree.get_common_ancestor("Larimichthys crocea - 215358", "Takifugu rubripes - 31033")
print(poly_1)
poly_2 = poly_1.resolve_polytomy(recursive=True)
print(poly_2)

gives "None", whereas it has following three nodes. ( Larimichthys crocea - 215358 ,Gasterosteus aculeatus - 69293 ,Takifugu rubripes - 31033 )

have tried with polytomy of four, but does not work either. (Nipponia nippon - 128390 , Columba livia - 8932 , Ficedula albicollis - 59894 , Haliaeetus leucocephalus - 52644 )

Also, is there any way to retrieve simple newick format from ete3's ncbi.get_topology() method?

from ete3 import NCBITaxa
ncbi = NCBITaxa()

tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
print tree.get_ascii(attributes=["sci_name", "rank"])

Any recommendations would be appreciated. referenced the following: http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#understanding-ete-trees http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#basic-tree-attributes http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-newick-trees http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2019/01/ete_tutorial.pdf http://etetoolkit.org/documentation/ete-ncbiquery/#ncbi_tree

ADD COMMENTlink modified 11 months ago by jhc2.8k • written 12 months ago by View70
0
gravatar for jhc
11 months ago by
jhc2.8k
Spain
jhc2.8k wrote:

not sure I understood the question, but hope the following points help:

  • resolves_politomies() does not return a new tree, it modifies the tree inplace.

  • the tree.standardize() function would be useful to remove one child nodes

  • to export a tree in newick, use tree.write() not tree.get_ascii()

ADD COMMENTlink written 11 months ago by jhc2.8k

I want to generate a binary tree from a list of species. in ete3 it is possible to generate a tree but it contains polytomies, which need to be resolved manually. I would like to know if there is a method to do this automatically for all the polytomies in a tree. since there are a lot of polytomies in some cases, it is time consuming to resolve one by one. After I asked the above question, I have used the following. As you see, it has to be done for every polytomy.

poly_1= tree.get_common_ancestor("Pongo abeli - 9601", "Gorilla gorilla - 9593")
poly_2= tree.get_common_ancestor("Nipponia nippon - 128390", "Columba livia - 8932")

poly_r = poly_1.resolve_polytomy(recursive=True)
poly_r = poly_2.resolve_polytomy(recursive=True)

Thanks for the tips!

ADD REPLYlink written 10 months ago by View70
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